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BMRB: 17613

2LCI

Solution NMR Structure of DE NOVO DESIGNED PROTEIN, P-LOOP NTPASE FOLD, Northeast Structural Genomics Consortium Target OR36

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Janjua, H., Ciccosanti, C., Lee, H., Acton, T.B., Everett, J., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium, N.

Assembly

OR36

Entity

1. OR36 (polymer, Thiol state: not present), 134 monomers, 16001.18 Da Detail

MKILILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIISND KQLLKEMLEL ISKLGYKVFL LLQDQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Formula weight

16001.18 Da

Exptl. method

solution NMR

Refine. method

distance geometry, molecular dynamics, torsion angle dynamics, simulated annealing

Data set

RDCs, assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 96.3 %, Completeness: 91.6 %, Completeness (bb): 91.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.6 % (1552 of 1694)	91.2 % (821 of 900)	91.9 % (593 of 645)	92.6 % (138 of 149)
Backbone	91.3 % (734 of 804)	90.8 % (247 of 272)	91.5 % (364 of 398)	91.8 % (123 of 134)
Sidechain	92.1 % (939 of 1020)	91.4 % (574 of 628)	92.8 % (350 of 377)	100.0 % (15 of 15)
Aromatic	65.9 % (58 of 88)	65.9 % (29 of 44)	65.9 % (29 of 44)
Methyl	100.0 % (150 of 150)	100.0 % (75 of 75)	100.0 % (75 of 75)

1. OR36

MKILILINTN NDELIKKIKK EVENQGYQVR DVNDSDELKK EMKKLAEEKN FEKILIISND KQLLKEMLEL ISKLGYKVFL LLQDQDENEL EEFKRKIESQ GYEVRKVTDD EEALKIVREF MQKAGSLEHH HHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.71mM OR36, NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.95mM OR36, NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
11	OR36	[U-10% 13C; U-100% 15N]	0.95 mM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %
14	NaN3	natural abundance	0.02 %
15	DTT	natural abundance	10 mM
16	CaCL2	natural abundance	5 mM
17	NaCL	natural abundance	100 mM
18	MES	natural abundance	20 mM
19	DSS	natural abundance	50 uM
20	Proteinase Inhibitors	natural abundance	1 na

Sample #3

#	Name	Isotope labeling	Concentration
21	OR36	[U-10% 13C; U-100% 15N]	0.95 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %
24	NaN3	natural abundance	0.02 %
25	DTT	natural abundance	10 mM
26	CaCL2	natural abundance	5 mM
27	NaCL	natural abundance	100 mM
28	MES	natural abundance	20 mM
29	DSS	natural abundance	50 uM
30	Proteinase Inhibitors	natural abundance	1 na

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: 0.15 ppm, Outliers: 1 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: 0.15 ppm, Outliers: 1 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: -0.06 ppm, Outliers: 5 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: 0.25 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LCI, Strand ID: A Detail

RDC

168 RDC values in 2 lists
Field strength (¹H) 599.520 MHz, Pressure 1 atm, Temperature 298 K, pH 6.5 Detail

Release date

2011-05-04

Citation

Role of backbone strain in de novo design of complex α/β protein structures
Koga, N., Koga, R., Liu, G., Castellanos, J., Montelione, G.T., Baker, D.
Nat. Commun. (2021), 12, 3921-3921, PubMed 34168113 , DOI 10.1038/s41467-021-24050-7 , Abstract

Related entities 1. OR36, : 1 : 2 : 8 entities Detail

Experiments performed 9 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.71mM OR36, NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 0.95mM OR36, NMR buffer 6.5 -- 0.02% NaN3, 10mM DTT, 5mM CaCL2, 100mM NaCL, 1x Proteinase Inhibitors, 20mM MES pH 6.5, 10% D2O, 50uM DSS

#	Name	Isotope labeling	Concentration
11	OR36	[U-10% 13C; U-100% 15N]	0.95 mM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %
14	NaN3	natural abundance	0.02 %
15	DTT	natural abundance	10 mM
16	CaCL2	natural abundance	5 mM
17	NaCL	natural abundance	100 mM
18	MES	natural abundance	20 mM
19	DSS	natural abundance	50 uM
20	Proteinase Inhibitors	natural abundance	1 na

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

7 3D simutaneous 13C-aromatic,13C-aliphatic,15N edited 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

#	Name	Isotope labeling	Concentration
1	OR36	[U-100% 13C; U-100% 15N]	0.71 mM
2	H2O	natural abundance	90 %
3	D2O	natural abundance	10 %
4	NaN3	natural abundance	0.02 %
5	DTT	natural abundance	10 mM
6	CaCL2	natural abundance	5 mM
7	NaCL	natural abundance	100 mM
8	MES	natural abundance	20 mM
9	DSS	natural abundance	50 uM
10	Proteinase Inhibitors	natural abundance	1 na

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
21	OR36	[U-10% 13C; U-100% 15N]	0.95 mM
22	H2O	natural abundance	90 %
23	D2O	natural abundance	10 %
24	NaN3	natural abundance	0.02 %
25	DTT	natural abundance	10 mM
26	CaCL2	natural abundance	5 mM
27	NaCL	natural abundance	100 mM
28	MES	natural abundance	20 mM
29	DSS	natural abundance	50 uM
30	Proteinase Inhibitors	natural abundance	1 na

9 2D HetNOE

Instrument

Varian INOVA - 600 MHz

Sample

#	Name	Isotope labeling	Concentration
11	OR36	[U-10% 13C; U-100% 15N]	0.95 mM
12	H2O	natural abundance	90 %
13	D2O	natural abundance	10 %
14	NaN3	natural abundance	0.02 %
15	DTT	natural abundance	10 mM
16	CaCL2	natural abundance	5 mM
17	NaCL	natural abundance	100 mM
18	MES	natural abundance	20 mM
19	DSS	natural abundance	50 uM
20	Proteinase Inhibitors	natural abundance	1 na

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17613_2lci.nef
Input source #2: Coordindates	2lci.cif
Diamagnetism of the molecular assembly	True (excluding Oxygen atoms)
Whether the assembly has a disulfide bond	None
Whether the assembly has a other bond	None
Whether the assembly contains a cyclic polymer	None
Overall data processing status	Warning

Disulfide bonds

None

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
MKILILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIISNDKQLLKEMLELISKLGYKVFLLLQDQDENELEEFKRKIESQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MKILILINTNNDELIKKIKKEVENQGYQVRDVNDSDELKKEMKKLAEEKNFEKILIISNDKQLLKEMLELISKLGYKVFLLLQDQDENELEEFKRKIESQ

-------110-------120-------130----
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH
||||||||||||||||||||||||||||||||||
GYEVRKVTDDEEALKIVREFMQKAGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	134	0	0	100.0

Content subtype: combined_17613_2lci.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1584		95.5 (chain: A, length: 134)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4492 (1)	noe	94.8 (chain: A, length: 134)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	58 (1)	hbond	36.6 (chain: A, length: 134)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	196 (196)	.	88.1 (chain: A, length: 134)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 95.5%
- Total number of assignments
  - ¹H chemical shifts: 847
  - ¹³C chemical shifts: 598
  - ¹⁵N chemical shifts: 139
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
9	THR	HG1	6.178
58	SER	HG	5.092

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	900	845	93.9
¹³C chemical shifts	645	598	92.7
¹⁵N chemical shifts	153	139	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	272	253	93.0
¹³C chemical shifts	268	246	91.8
¹⁵N chemical shifts	134	122	91.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	628	592	94.3
¹³C chemical shifts	377	352	93.4
¹⁵N chemical shifts	19	17	89.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	79	78	98.7
¹³C chemical shifts	79	78	98.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	44	29	65.9
¹³C chemical shifts	44	29	65.9

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 134, Sequence coverage: 94.8%
- Total number of restraints: 4480
- Weight of restraints: 1.0 (4480)
- Potential type of restraints: square-well-parabolic (4480)
- Range of distance target values: 2.15, 4.46 (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: 134, Sequence coverage: 36.6%
  - Total number of restraints: 58
  - Weight of restraints: 1.0 (58)
  - Potential type of restraints: square-well-parabolic (58)
  - Range of distance target values: 1.99, 2.99 (Å)
  - Histogram of distance target values
  - 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: 134, Sequence coverage: 88.1%
- Total number of restraints: 196
- Total number of restraints per polymer type: 196
- Weight of restraints: 1.0 (196)
- Potential type of restraints: square-well-parabolic (196)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords Denovo Design, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, Structural Genomics, Target OR36

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Found 1 Document (0.72 seconds)

BMRB: 17613

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. OR36, : 1 : 2 : 8 entities Detail

Experiments performed 9 experiments Detail

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NMR combined restraints 5 contents Detail