BMRBj - BMREntryMaster

Found 1 Document (0.781 seconds)

BMRB: 18541

2LUU

NMR solution structure of midkine-b, mdkb

Authors

Yang, D., Lim, J., Meng, D.

Assembly

midkine-b

Entity

1. midkine-b (polymer, Thiol state: all disulfide bound), 127 monomers, 13989.90 Da Detail

GSMKKKEKGK EPKADAECSE WQYGKCVPNS GDCGNGIREA TCNEQTKKTK CKVPCNWKKD FGADCKYKFG RWAECDTTTG TRSRSGTLKK ALFNAECQTT IKVSKPCTPK TPKPKGGEKK KGKGKEN

Formula weight

13989.9 Da

Entity Connection

disulfide 5 Detail

ID	Type	Value order	Atom ID 1	Atom ID 2
1	disulfide	sing	1:CYS18:SG	1:CYS42:SG
2	disulfide	sing	1:CYS26:SG	1:CYS51:SG
3	disulfide	sing	1:CYS33:SG	1:CYS55:SG
4	disulfide	sing	1:CYS65:SG	1:CYS97:SG
5	disulfide	sing	1:CYS75:SG	1:CYS107:SG

Source organism

Danio rerio

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 69.6 %, Completeness (bb): 77.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	69.6 % (1029 of 1478)	68.6 % (544 of 793)	66.2 % (366 of 553)	90.2 % (119 of 132)
Backbone	77.3 % (578 of 748)	88.5 % (231 of 261)	64.6 % (237 of 367)	91.7 % (110 of 120)
Sidechain	65.2 % (550 of 843)	58.8 % (313 of 532)	76.3 % (228 of 299)	75.0 % (9 of 12)
Aromatic	80.5 % (66 of 82)	80.5 % (33 of 41)	78.9 % (30 of 38)	100.0 % (3 of 3)
Methyl	97.0 % (64 of 66)	97.0 % (32 of 33)	97.0 % (32 of 33)

1. midkine-b

GSMKKKEKGK EPKADAECSE WQYGKCVPNS GDCGNGIREA TCNEQTKKTK CKVPCNWKKD FGADCKYKFG RWAECDTTTG TRSRSGTLKK ALFNAECQTT IKVSKPCTPK TPKPKGGEKK KGKGKEN

Show sample condition

Sample

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM NaH2PO4/ Na2HPO4 at pH 6.5, 0.1 mM NaN3, 100 mM NaCl, 1 mM EDTA, 95% H2O, 5 % D2O

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: -0.2 ppm, Outliers: 1 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Value	Ref. method	Ref. type	Shift ratio
¹³C	DSS	methyl protons	0.0 ppm	na	indirect	0.2514495
¹H	water	protons	4.71 ppm	external	indirect	1.0
¹⁵N	DSS	methyl protons	0.0 ppm	na	indirect	0.1013291

Referencing offset: 0.04 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2LUU, Strand ID: A Detail

Release date

2013-04-01

Citation

Structure-function analysis of full-length midkine reveals novel residues important for heparin binding and zebrafish embryogenesis
Lim, J., Yao, S., Graf, M., Winkler, C., Yang, D.
Biochem. J. (2013), 451, 407-415, PubMed 23418741 , DOI 10.1042/BJ20121622 , Abstract

Related entities 1. midkine-b, : 1 : 1 : 9 entities Detail

Experiments performed 6 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 10 mM NaH2PO4/ Na2HPO4 at pH 6.5, 0.1 mM NaN3, 100 mM NaCl, 1 mM EDTA, 95% H2O, 5 % D2O

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

3 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

4 3D HNCA

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

5 3D MQ-(H)CCH-TOCSY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

6 4D timeshared 13C/ 15N edited NOESY

Instrument

Bruker Avance - 500 MHz

Sample

#	Name	Isotope labeling	Concentration
1	potassium phosphate	natural abundance	10 mM
2	sodium azide	natural abundance	0.1 mM
3	sodium chloride	natural abundance	100 mM
4	EDTA	natural abundance	1 mM
5	midkine-b	[U-100% 13C; U-100% 15N]	0.8 mM
6	H2O	natural abundance	95 %
7	D2O	natural abundance	5 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18541_2luu.nef
Input source #2: Coordindates	2luu.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:18:CYS:SG	A:42:CYS:SG	oxidized, CA 57.84, CB 42.356 ppm	oxidized, CA 56.3, CB 39.97 ppm	1.998
A:26:CYS:SG	A:51:CYS:SG	oxidized, CA 55.866, CB 41.272 ppm	oxidized, CA 55.06, CB 47.407 ppm	1.998
A:33:CYS:SG	A:55:CYS:SG	oxidized, CA 56.238, CB 48.12 ppm	reduced, CA 54.306, CB 31.635 ppm	1.99
A:65:CYS:SG	A:97:CYS:SG	oxidized, CA 53.526, CB 41.489 ppm	oxidized, CA 53.759, CB 44.03 ppm	1.979
A:75:CYS:SG	A:107:CYS:SG	oxidized, CA 57.361, CB 41.364 ppm	oxidized, CA 55.948, CB 45.021 ppm	2.105

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
GSMKKKEKGKEPKADAECSEWQYGKCVPNSGDCGNGIREATCNEQTKKTKCKVPCNWKKDFGADCKYKFGRWAECDTTTGTRSRSGTLKKALFNAECQTT
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GSMKKKEKGKEPKADAECSEWQYGKCVPNSGDCGNGIREATCNEQTKKTKCKVPCNWKKDFGADCKYKFGRWAECDTTTGTRSRSGTLKKALFNAECQTT

-------110-------120-------
IKVSKPCTPKTPKPKGGEKKKGKGKEN
|||||||||||||||||||||||||||
IKVSKPCTPKTPKPKGGEKKKGKGKEN

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	127	0	0	100.0

Content subtype: combined_18541_2luu.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Covalent bonds	assembly	OK	5		No information
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	947		92.1 (chain: A, length: 127)
1	Distance restraints	DYANA/DIANA_distance_constraints_4	Warning	2824 (1)	noe	85.8 (chain: A, length: 127)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_2	OK	99 (99)	.	66.1 (chain: A, length: 127)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 92.1%
- Total number of assignments
  - ¹H chemical shifts: 501
  - ¹³C chemical shifts: 331
  - ¹⁵N chemical shifts: 115
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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 (%)
¹H chemical shifts	793	501	63.2
¹³C chemical shifts	553	331	59.9
¹⁵N chemical shifts	136	115	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	261	224	85.8
¹³C chemical shifts	254	113	44.5
¹⁵N chemical shifts	120	106	88.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	532	277	52.1
¹³C chemical shifts	299	218	72.9
¹⁵N chemical shifts	16	9	56.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	34	32	94.1
¹³C chemical shifts	34	32	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	41	31	75.6
¹³C chemical shifts	38	28	73.7
¹⁵N chemical shifts	3	3	100.0

Covalent bonds

Saveframe: assembly
- Status: OK

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_4
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 85.8%
- Total number of restraints: 2824
- Weight of restraints: 1.0 (2824)
- Potential type of restraints: upper-bound-parabolic (2824)
- Range of distance target values: 1.8, 5.5 (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

Dihedral angle restraints

Saveframe: DYANA/DIANA_dihedral_2
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 127, Sequence coverage: 66.1%
- Total number of restraints: 99
- Total number of restraints per polymer type: 99
- Weight of restraints: 1.0 (99)
- Potential type of restraints: square-well-parabolic (99)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords beta sheet, disulfide bond, independent half-domain, midkine

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.781 seconds)

BMRB: 18541

Sample

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. midkine-b, : 1 : 1 : 9 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail