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Found 1 Document (0.756 seconds)

BMRB: 17275

2L5L

Solution Structure of Thioredoxin from Bacteroides Vulgatus

Authors

Harris, R., Foti, R., Seidel, R.D., Bonanno, J.B., Freeman, J., Bain, K.T., Sauder, J.M., Burley, S.K., Girvin, M.E., Almo, S.C., Harris, R.

Assembly

thioredoxin

Entity

1. thioredoxin (polymer, Thiol state: all free), 136 monomers, 15402.55 Da Detail

MSLATEGNGK VIHLTKAEFL AKVYNFEKNP EEWKYEGDKP AIVDFYADWC GPCKMVAPIL DELAKEYDGQ IVIYKVDTEK EQELAGAFGI RSIPSILFIP MEGKPEMAQG AMPKASFKKA IDEFLLKKEG HHHHHH

Formula weight

15402.55 Da

Source organism

Phocaeicola vulgatus

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.9 %, Completeness: 91.2 %, Completeness (bb): 91.1 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.2 % (1488 of 1632)	89.9 % (767 of 853)	92.7 % (596 of 643)	91.9 % (125 of 136)
Backbone	91.1 % (729 of 800)	88.3 % (242 of 274)	93.0 % (370 of 398)	91.4 % (117 of 128)
Sidechain	91.5 % (877 of 958)	90.7 % (525 of 579)	92.7 % (344 of 371)	100.0 % (8 of 8)
Aromatic	79.6 % (129 of 162)	77.8 % (63 of 81)	81.0 % (64 of 79)	100.0 % (2 of 2)
Methyl	98.5 % (130 of 132)	97.0 % (64 of 66)	100.0 % (66 of 66)

1. thioredoxin

MSLATEGNGK VIHLTKAEFL AKVYNFEKNP EEWKYEGDKP AIVDFYADWC GPCKMVAPIL DELAKEYDGQ IVIYKVDTEK EQELAGAFGI RSIPSILFIP MEGKPEMAQG AMPKASFKKA IDEFLLKKEG HHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
7	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

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: -0.32 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: -0.32 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: -0.06 ppm, Outliers: 3 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: 0.06 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L5L, Strand ID: A Detail

Release date

2010-11-14

Related entities 1. thioredoxin, : 1 : 102 entities Detail

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

2 15N NOESY-HSQC

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
7	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
7	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

5 13C NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
7	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
7	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	50 mM
10	DTT	natural abundance	1 mM
11	D2O	natural abundance	100 %

7 HNCO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 HNCACO

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 HNCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 HNCOCA

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 HNCACB

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 CBCACONH

Instrument

Bruker DRX - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17275_2l5l.nef
Input source #2: Coordindates	2l5l.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
MSLATEGNGKVIHLTKAEFLAKVYNFEKNPEEWKYEGDKPAIVDFYADWCGPCKMVAPILDELAKEYDGQIVIYKVDTEKEQELAGAFGIRSIPSILFIP
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLATEGNGKVIHLTKAEFLAKVYNFEKNPEEWKYEGDKPAIVDFYADWCGPCKMVAPILDELAKEYDGQIVIYKVDTEKEQELAGAFGIRSIPSILFIP

-------110-------120-------130------
MEGKPEMAQGAMPKASFKKAIDEFLLKKEGHHHHHH
||||||||||||||||||||||||||||||||||||
MEGKPEMAQGAMPKASFKKAIDEFLLKKEGHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	136	0	0	100.0

Content subtype: combined_17275_2l5l.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1526		94.9 (chain: A, length: 136)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2718 (1)	noe	94.1 (chain: A, length: 136)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	208 (1)	noe	58.8 (chain: A, length: 136)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	74 (1)	hbond	39.0 (chain: A, length: 136)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	189 (189)	.	87.5 (chain: A, length: 136)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 94.9%
- Total number of assignments
  - ¹H chemical shifts: 800
  - ¹³C chemical shifts: 602
  - ¹⁵N chemical shifts: 124
- 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 (%)
¹H chemical shifts	853	800	93.8
¹³C chemical shifts	643	602	93.6
¹⁵N chemical shifts	137	124	90.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	274	255	93.1
¹³C chemical shifts	272	255	93.8
¹⁵N chemical shifts	128	116	90.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	579	545	94.1
¹³C chemical shifts	371	347	93.5
¹⁵N chemical shifts	9	8	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	71	70	98.6
¹³C chemical shifts	71	70	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	81	68	84.0
¹³C chemical shifts	79	66	83.5
¹⁵N chemical shifts	2	2	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: 136, Sequence coverage: 94.1%
- Total number of restraints: 2703
- Weight of restraints: 1.0 (2703)
- Potential type of restraints: square-well-parabolic (2703)
- Range of distance target values: 2.4, 4.15 (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_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 58.8%
  - Total number of restraints: 205
  - Weight of restraints: 1.0 (205)
  - Potential type of restraints: square-well-parabolic (205)
  - Range of distance target values: 2.4, 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: 136, Sequence coverage: 39.0%
    - Total number of restraints: 74
    - Weight of restraints: 1.0 (74)
    - Potential type of restraints: square-well-parabolic (74)
    - Range of distance target values: 2.05, 3.05 (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_5
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 136, Sequence coverage: 87.5%
- Total number of restraints: 189
- Total number of restraints per polymer type: 189
- Weight of restraints: 1.0 (189)
- Potential type of restraints: square-well-parabolic (189)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords ELECTRON TRANSPORT, STRUCTURAL GENOMICS, New York SGX Research Center for Structural Genomics, Protein Structure Initiative, PSI-2

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Found 1 Document (0.756 seconds)

BMRB: 17275

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. thioredoxin, : 1 : 102 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail