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Found 1 Document (0.742 seconds)

BMRB: 18145

2LN3

Solution NMR Structure of DE NOVO DESIGNED PROTEIN, IF3-like fold, Northeast Structural Genomics Consortium Target OR135 (CASD target)

Authors

Liu, G., Koga, N., Koga, R., Xiao, R., Lee, H., Janjua, H., Kohan, E., Acton, T.B., Everett, J.K., Baker, D., Montelione, G.T.

Assembly

OR135

Entity

1. OR135 (polymer, Thiol state: not present), 83 monomers, 9778.871 Da Detail

MGLTRTITSQ NKEELLEIAL KFISQGLDLE VEFDSTDDKE IEEFERDMED LAKKTGVQIQ KQWQGNKLRI RLKGSLEHHH HHH

Formula weight

9778.871 Da

Exptl. method

solution NMR

Refine. method

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

Data set

assigned_chemical_shifts, RDCs

Chem. Shift Complete

Sequence coverage: 94.0 %, Completeness: 89.8 %, Completeness (bb): 88.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	89.8 % (907 of 1010)	90.0 % (479 of 532)	89.6 % (346 of 386)	89.1 % (82 of 92)
Backbone	88.4 % (440 of 498)	86.5 % (148 of 171)	89.8 % (219 of 244)	88.0 % (73 of 83)
Sidechain	90.3 % (533 of 590)	90.3 % (326 of 361)	90.0 % (198 of 220)	100.0 % (9 of 9)
Aromatic	66.7 % (44 of 66)	69.7 % (23 of 33)	62.5 % (20 of 32)	100.0 % (1 of 1)
Methyl	100.0 % (86 of 86)	100.0 % (43 of 43)	100.0 % (43 of 43)

1. OR135

MGLTRTITSQ NKEELLEIAL KFISQGLDLE VEFDSTDDKE IEEFERDMED LAKKTGVQIQ KQWQGNKLRI RLKGSLEHHH HHH

Show sample condition

Sample #1

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

Sample #2

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.14 mM [U-5% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	OR135	[U-5% 13C; U-100% 15N]	1.14 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

Sample #3

Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.14 mM [U-5% 13C; U-100% 15N]; 95% H2O/5% D2O Alignment media: Peg or phage

#	Name	Isotope labeling	Concentration
7	OR135	[U-5% 13C; U-100% 15N]	1.14 mM
8	OR135	natural abundance	95 %
9	OR135	natural abundance	5 %

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: 0.07 ppm, Outliers: 1 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: 0.07 ppm, Outliers: 1 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: -0.11 ppm, Outliers: 1 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: 0.22 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LN3, Strand ID: A Detail

RDC

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

Release date

2012-01-30

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: 18465 released on 2012-06-10
    Title SOLUTION NMR STRUCTURE OF DE NOVO DESIGNED PROTEIN, ROSSMANN 3x1 FOLD, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET OR157
  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. OR135, : 1 : 8 entities Detail

Experiments performed 10 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

2 2D 1H-13C HSQC

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

3 3D HNCO

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

4 3D CBCA(CO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

6 3D 1H-13C arom NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

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

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

8 2D 1H-13C HSQC aliphatic

Instrument

Varian INOVA - 600 MHz at Rutgers

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.14 mM [U-5% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	OR135	[U-5% 13C; U-100% 15N]	1.14 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

9 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz at UGA

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.14 mM [U-5% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
4	OR135	[U-5% 13C; U-100% 15N]	1.14 mM
5	H2O	natural abundance	95 %
6	D2O	natural abundance	5 %

10 3D HCCH-TOCSY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 95% H2O/5% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5, Details 1.04 mM [U-100% 13C; U-100% 15N]; 95% H2O/5% D2O

#	Name	Isotope labeling	Concentration
1	OR135	[U-100% 13C; U-100% 15N]	1.04 mM
2	H20	natural abundance	95 %
3	D20	natural abundance	5 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18145_2ln3.nef
Input source #2: Coordindates	2ln3.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---
MGLTRTITSQNKEELLEIALKFISQGLDLEVEFDSTDDKEIEEFERDMEDLAKKTGVQIQKQWQGNKLRIRLKGSLEHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MGLTRTITSQNKEELLEIALKFISQGLDLEVEFDSTDDKEIEEFERDMEDLAKKTGVQIQKQWQGNKLRIRLKGSLEHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	83	0	0	100.0

Content subtype: combined_18145_2ln3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	928		92.8 (chain: A, length: 83)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	4096 (1)	noe	90.4 (chain: A, length: 83)
2	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	70 (1)	hbond	53.0 (chain: A, length: 83)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	108 (108)	.	79.5 (chain: A, length: 83)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 83, Sequence coverage: 92.8%
- Total number of assignments
  - ¹H chemical shifts: 492
  - ¹³C chemical shifts: 351
  - ¹⁵N chemical shifts: 85
- 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)
35	SER	HG	5.887

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	532	491	92.3
¹³C chemical shifts	386	351	90.9
¹⁵N chemical shifts	96	85	88.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	171	155	90.6
¹³C chemical shifts	166	150	90.4
¹⁵N chemical shifts	83	74	89.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	361	336	93.1
¹³C chemical shifts	220	201	91.4
¹⁵N chemical shifts	13	11	84.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	45	44	97.8
¹³C chemical shifts	45	44	97.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	33	23	69.7
¹³C chemical shifts	32	20	62.5
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: 83, Sequence coverage: 90.4%
- Total number of restraints: 4085
- Weight of restraints: 1.0 (4085)
- Potential type of restraints: square-well-parabolic (4085)
- Range of distance target values: 2.19, 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: 83, Sequence coverage: 53.0%
  - Total number of restraints: 70
  - Weight of restraints: 1.0 (70)
  - Potential type of restraints: square-well-parabolic (70)
  - 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: 83, Sequence coverage: 79.5%
- Total number of restraints: 108
- Total number of restraints per polymer type: 108
- Weight of restraints: 1.0 (108)
- Potential type of restraints: square-well-parabolic (108)
- 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 OR135

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Found 1 Document (0.742 seconds)

BMRB: 18145

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. OR135, : 1 : 8 entities Detail

Experiments performed 10 experiments Detail

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NMR combined restraints 5 contents Detail