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Found 1 Document (0.735 seconds)

BMRB: 18465

2LTA

SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, ROSSMANN 3x1 FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR157

Authors

Liu, G., Koga, R., Koga, N., Xiao, R., Pederson, K., Hamilton, K., Kohan, E., Acton, T.B., Kornhaber, G., Everett, J.K., Baker, D., Montelione, G.T., Northeast Structural Genomics Consortium, N.

Assembly

OR157

Entity

1. OR157 (polymer, Thiol state: not present), 110 monomers, 13033.75 Da Detail

MGSKIIVIIS SDDTTLEELA RKIKDEGLEV YILLKDKDEK RLEEKIQKLK SQGFEVRKVK DDDDIDKWID KIKKERPQLE VRKVTDEDQA KQILEDLKKK GSLEHHHHHH

Formula weight

13033.75 Da

Exptl. method

solution NMR

Refine. method

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

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.5 %, Completeness: 92.6 %, Completeness (bb): 91.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.6 % (1269 of 1370)	92.7 % (677 of 730)	92.6 % (486 of 525)	92.2 % (106 of 115)
Backbone	91.8 % (604 of 658)	91.0 % (203 of 223)	92.3 % (301 of 326)	91.7 % (100 of 109)
Sidechain	93.4 % (764 of 818)	93.5 % (474 of 507)	93.1 % (284 of 305)	100.0 % (6 of 6)
Aromatic	55.6 % (30 of 54)	55.6 % (15 of 27)	53.8 % (14 of 26)	100.0 % (1 of 1)
Methyl	100.0 % (122 of 122)	100.0 % (61 of 61)	100.0 % (61 of 61)

1. OR157

MGSKIIVIIS SDDTTLEELA RKIKDEGLEV YILLKDKDEK RLEEKIQKLK SQGFEVRKVK DDDDIDKWID KIKKERPQLE VRKVTDEDQA KQILEDLKKK GSLEHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.805 mM OR157.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	OR157.006	[U-100% 13C; U-100% 15N]	0.805 mM
9	NaCl	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	NaN3	natural abundance	0.02 %
12	Tris-HCl pH 7.5	natural abundance	10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

Sample #3

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.805 mM OR157.008, 90% H2O/10% D2O, alignment media: phase or peg/hexanol

#	Name	Isotope labeling	Concentration
15	OR157.006	[U-100% 13C; U-100% 15N]	0.805 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

LACS Plot; CA

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

Referencing offset: 0.08 ppm, Outliers: 2 Detail

LACS Plot; CB

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

Referencing offset: 0.08 ppm, Outliers: 2 Detail

LACS Plot; HA

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

Referencing offset: -0.05 ppm, Outliers: 2 Detail

LACS Plot; CO

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

Referencing offset: 0.08 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-06-10

Citation

Principles for designing ideal protein structures
Koga, N., Tatsumi-Koga, R., Liu, G., Xiao, R., Acton, T.B., Montelione, G.T., Baker, D.
Nature (2012), 491, 222-227, PubMed 23135467 , DOI 10.1038/nature11600 , Abstract

Entries sharing articles BMRB: 4 entries Detail

  BMRB: 18558 released on 2012-07-30
    Title Solution NMR Structure de novo designed rossmann 2x2 fold protein, Northeast Structural Genomics Consortium (NESG) Target OR16
  BMRB: 18561 released on 2012-07-09
    Title Solution NMR Structure DE NOVO DESIGNED PFK fold PROTEIN, Northeast Structural Genomics Consortium (NESG) Target OR250
  BMRB: 18145 released on 2012-01-30
    Title Solution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold, Northeast Structural Genomics Consortium Target OR135 (CASD target)
  BMRB: 16387 released on 2009-08-05
    Title Solution NMR Structure of denovo designed ferrodoxin fold like protein, Northeast Structural Genomics Consortium Target Target OR15

Related entities 1. OR157, : 1 : 18 entities Detail

Experiments performed 10 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 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.805 mM OR157.006, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
8	OR157.006	[U-100% 13C; U-100% 15N]	0.805 mM
9	NaCl	natural abundance	100 mM
10	DTT	natural abundance	5 mM
11	NaN3	natural abundance	0.02 %
12	Tris-HCl pH 7.5	natural abundance	10 mM
13	H2O	natural abundance	90 %
14	D2O	natural abundance	10 %

3 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

5 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

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

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

8 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 0.805 mM OR157.008, 90% H2O/10% D2O, alignment media: phase or peg/hexanol

#	Name	Isotope labeling	Concentration
15	OR157.006	[U-100% 13C; U-100% 15N]	0.805 mM
16	NaCl	natural abundance	100 mM
17	DTT	natural abundance	5 mM
18	NaN3	natural abundance	0.02 %
19	Tris-HCl pH 7.5	natural abundance	10 mM
20	H2O	natural abundance	90 %
21	D2O	natural abundance	10 %

9 3D HBHA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	D2O	natural abundance	10 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5, Details 1.035 mM OR157.004, 90% H2O/10% D2O

#	Name	Isotope labeling	Concentration
1	OR157.004	[U-100% 13C; U-100% 15N]	1.035 mM
2	NaCl	natural abundance	100 mM
3	DTT	natural abundance	5 mM
4	NaN3	natural abundance	0.02 %
5	Tris-HCl pH 7.5	natural abundance	10 mM
6	H2O	natural abundance	90 %
7	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_18465_2lta.nef
Input source #2: Coordindates	2lta.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
MGSKIIVIISSDDTTLEELARKIKDEGLEVYILLKDKDEKRLEEKIQKLKSQGFEVRKVKDDDDIDKWIDKIKKERPQLEVRKVTDEDQAKQILEDLKKK
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGSKIIVIISSDDTTLEELARKIKDEGLEVYILLKDKDEKRLEEKIQKLKSQGFEVRKVKDDDDIDKWIDKIKKERPQLEVRKVTDEDQAKQILEDLKKK

-------110
GSLEHHHHHH
||||||||||
GSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	110	0	0	100.0

Content subtype: combined_18465_2lta.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1266		94.5 (chain: A, length: 110)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4560 (1)	noe	92.7 (chain: A, length: 110)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	38 (1)	hbond	33.6 (chain: A, length: 110)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	164 (164)	.	88.2 (chain: A, length: 110)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 94.5%
- Total number of assignments
  - ¹³C chemical shifts: 483
  - ¹H chemical shifts: 678
  - ¹⁵N chemical shifts: 105
- Completeness of assignments
  - Entity_assemble_ID: A
- 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 (%)
¹³C chemical shifts	525	483	92.0
¹H chemical shifts	730	678	92.9
¹⁵N chemical shifts	120	105	87.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	220	200	90.9
¹H chemical shifts	223	205	91.9
¹⁵N chemical shifts	109	99	90.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	305	283	92.8
¹H chemical shifts	507	473	93.3
¹⁵N chemical shifts	11	6	54.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	62	61	98.4
¹H chemical shifts	62	61	98.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹³C chemical shifts	26	14	53.8
¹H chemical shifts	27	15	55.6
¹⁵N chemical shifts	1	1	100.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 110, Sequence coverage: 92.7%
- Total number of restraints: 4549
- Weight of restraints: 1.0 (4549)
- Potential type of restraints: square-well-parabolic (4549)
- Range of distance target values: 2.15, 4.35 (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: 110, Sequence coverage: 33.6%
  - Total number of restraints: 38
  - Weight of restraints: 1.0 (38)
  - Potential type of restraints: square-well-parabolic (38)
  - 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: 110, Sequence coverage: 88.2%
- Total number of restraints: 164
- Total number of restraints per polymer type: 164
- Weight of restraints: 1.0 (164)
- Potential type of restraints: square-well-parabolic (164)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords NORTHEAST STRUCTURAL GENOMICS CONSORTIUM (NESG), Protein NMR, Protein Structure Initiative, PSI-Biology, Structural Genomics, Target OR157

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Found 1 Document (0.735 seconds)

BMRB: 18465

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Entries sharing articles BMRB: 4 entries Detail

Related entities 1. OR157, : 1 : 18 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail