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Found 1 Document (1.34 seconds)

BMRB: 15964

2K8V

Solution structure of Oxidised ERp18

Authors

Rowe, M.L., Alanen, H.I., Ruddock, L.W., Kelly, G., Schmidt, J.M., Williamson, R.A., Howard, M.J.

Assembly

ERp18

Entity

1. ERp18 (polymer, Thiol state: all disulfide bound), 157 monomers, 17770.70 Da Detail

MHHHHHHMSD GHNGLGKGFG DHIHWRTLED GKKEAAASGL PLMVIIHKSW CGACKALKPK FAESTEISEL SHNFVMVNLE DEEEPKDEDF SPDGGYIPRI LFLDPSGKVH PEIINENGNP SYKYFYVSAE QVVQGMKEAQ ERLTGDAFRK KHLEDEL

Formula weight

17770.7 Da

Entity Connection

disulfide 1 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS51:SG	1:CYS54:SG

Source organism

Homo sapiens

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.5 %, Completeness: 89.2 %, Completeness (bb): 92.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.2 % (1632 of 1830)	92.4 % (883 of 956)	83.9 % (599 of 714)	93.8 % (150 of 160)
Backbone	92.2 % (854 of 926)	92.8 % (297 of 320)	91.5 % (418 of 457)	93.3 % (139 of 149)
Sidechain	87.2 % (913 of 1047)	92.1 % (586 of 636)	79.0 % (316 of 400)	100.0 % (11 of 11)
Aromatic	58.4 % (104 of 178)	85.4 % (76 of 89)	29.9 % (26 of 87)	100.0 % (2 of 2)
Methyl	100.0 % (132 of 132)	100.0 % (66 of 66)	100.0 % (66 of 66)

1. ERp18

MHHHHHHMSD GHNGLGKGFG DHIHWRTLED GKKEAAASGL PLMVIIHKSW CGACKALKPK FAESTEISEL SHNFVMVNLE DEEEPKDEDF SPDGGYIPRI LFLDPSGKVH PEIINENGNP SYKYFYVSAE QVVQGMKEAQ ERLTGDAFRK KHLEDEL

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
1	ERp18	[U-99% 15N]	0.7-1.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 %
4	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
9	ERp18	[U-99% 13C; U-99% 15N]	0.7-1.5 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	100 %
12	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.21 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.02 ppm, Outliers: 1 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: 0.0 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 40 models in PDB: 2K8V, Strand ID: A Detail

Release date

2009-04-21

Citation 1

Solution structure and dynamics of ERp18, a small endoplasmic reticulum resident oxidoreductase
Rowe, M.L., Ruddock, L.W., Kelly, G., Schmidt, J.M., Williamson, R.A., Howard, M.J.
Biochemistry (2009), 48, 4596-4606, PubMed 19361226 , DOI 10.1021/bi9003342 , Abstract

Show more 1 citaion

Citation 2

Functional characterization of ERp18, a new endoplasmic reticulum-located thioredoxin superfamily member
Alanen, H.I., Williamson, R.A., Howard, M.J., Lappi, A., Jantti, H.P., Rautio, S.M., Kellokupu, S., Ruddock, L.W.
J. Biol. Chem. (2003), 278, 28912-28920, PubMed 12761212 , DOI 10.1074/jbc.M304598200 , Abstract

Hide non-primary 1 citaion

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

  BMRB: 7430 released on 2009-04-21
    Title Solution structure of Reduced ERp18
  Swiss-Prot: O95881 released on 2003-04-11
    Title TXD12_HUMAN Entity Thioredoxin domain-containing protein 12

Related entities 1. ERp18, : 1 : 2 : 34 entities Detail

Interaction partners 1. ERp18, : 6 interactors Detail

More details for 6 interactors identified by 3 citations

Experiments performed 13 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
1	ERp18	[U-99% 15N]	0.7-1.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 %
4	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

4 3D HNCACB

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

5 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

6 3D HBHANH

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

7 3D HNCO

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
9	ERp18	[U-99% 13C; U-99% 15N]	0.7-1.5 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	100 %
12	D2O	natural abundance	100 %

11 3D 1H-15N TOCSY

Instrument

Varian INOVA - 600 MHz University of Kent; 5mm HCN z-pulse field gradient probe

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
1	ERp18	[U-99% 15N]	0.7-1.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 %
4	D2O	natural abundance	10 %

12 3D 1H-15N NOESY

Instrument

Varian INOVA - 800 MHz NIMR, Mill Hill

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
1	ERp18	[U-99% 15N]	0.7-1.5 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 %
4	D2O	natural abundance	10 %

13 3D 1H-13C NOESY

Instrument

Varian INOVA - 800 MHz NIMR, Mill Hill

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details Sample Oxidised prior to concentration using 0.5 mM GSSG

#	Name	Isotope labeling	Concentration
5	ERp18	[U-99% 13C; U-99% 15N]	1-1.5 mM
6	sodium phosphate	natural abundance	20 mM
7	sodium chloride	natural abundance	100 %
8	D2O	natural abundance	10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_15964_2k8v.nef
Input source #2: Coordindates	2k8v.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	True (see coordinates for details)
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

Ptnr_site_1	Ptnr_site_2	Redox_state_prediction_1	Redox_state_prediction_2	Distance (Å)
A:51:CYS:SG	A:54:CYS:SG	unknown	oxidized 2.9%, reduced 97.1%, CA 63.583, CB 33.572 ppm	2.031

Other bonds (neither disulfide, covalent nor hydrogen bonds, e.g. Zinc–sulphur bond)

None

Non-standard residues

None

Sequence alignments

Entity_assembly_ID (NMR): A vs Auth_asym_ID (model): A

--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100
MHHHHHHMSDGHNGLGKGFGDHIHWRTLEDGKKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPRI
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHHHHHHMSDGHNGLGKGFGDHIHWRTLEDGKKEAAASGLPLMVIIHKSWCGACKALKPKFAESTEISELSHNFVMVNLEDEEEPKDEDFSPDGGYIPRI

-------110-------120-------130-------140-------150-------
LFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFRKKHLEDEL
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LFLDPSGKVHPEIINENGNPSYKYFYVSAEQVVQGMKEAQERLTGDAFRKKHLEDEL

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	157	0	0	100.0

Content subtype: combined_15964_2k8v.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	1		No information
1	Assigned chemical shifts	Oxidised_ERp18	Warning	1626		95.5 (chain: A, length: 157)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3232 (1)	noe	93.0 (chain: A, length: 157)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	58 (1)	hbond	50.3 (chain: A, length: 157)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	153 (153)	.	58.6 (chain: A, length: 157)

Assigned chemical shifts

Saveframe: Oxidised_ERp18
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 95.5%
- Total number of assignments
  - ¹³C chemical shifts: 589
  - ¹H chemical shifts: 888
  - ¹⁵N chemical shifts: 149
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- Tautomeric state of HIS
- Rotameric state of ILE , LEU, and VAL
- Histogram of normalized assigned chemical shifts
- Random coil index and derived parameters (S² and NMR RMSD)
  - Chain_ID: A

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	714	589	82.5
¹H chemical shifts	956	884	92.5
¹⁵N chemical shifts	164	149	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	314	280	89.2
¹H chemical shifts	320	300	93.8
¹⁵N chemical shifts	149	138	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	400	309	77.2
¹H chemical shifts	636	584	91.8
¹⁵N chemical shifts	15	11	73.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	71	66	93.0
¹H chemical shifts	71	69	97.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	87	23	26.4
¹H chemical shifts	89	77	86.5
¹⁵N chemical shifts	2	2	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 93.0%
- Total number of restraints: 3230
- Weight of restraints: 1.0 (3230)
- Potential type of restraints: square-well-parabolic (3230)
- Range of distance target values: 2.15, 3.9 (Å)
- Histogram of distance target values
- Histogram of discrepancy in distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_4
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 50.3%
  - Total number of restraints: 58
  - Weight of restraints: 1.0 (58)
  - Potential type of restraints: square-well-parabolic (58)
  - Range of distance target values: 2.2, 2.2 (Å)
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 157, Sequence coverage: 58.6%
- Total number of restraints: 153
- Total number of restraints per polymer type: 153
- Weight of restraints: 1.0 (153)
- Potential type of restraints: square-well-parabolic (153)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords endoplasmic reticulum, oxidase, thioredoxin fold

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Found 1 Document (1.34 seconds)

BMRB: 15964

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 1, Swiss-Prot: 1 entries Detail

Related entities 1. ERp18, : 1 : 2 : 34 entities Detail

Interaction partners 1. ERp18, : 6 interactors Detail

Experiments performed 13 experiments Detail

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NMR combined restraints 5 contents Detail