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BMRB: 17277

2L5O

Solution Structure of a Putative Thioredoxin from Neisseria meningitidis

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.

Assembly

putative thioredoxin

Entity

1. putative thioredoxin (polymer, Thiol state: all free), 153 monomers, 17024.09 Da Detail

MSLDSKTAPA FSLPDLHGKT VSNADLQGKV TLINFWFPSC PGCVSEMPKI IKTANDYKNK NFQVLAVAQP IDPIESVRQY VKDYGLPFTV MYDADKAVGQ AFGTQVYPTS VLIGKKGEIL KTYVGEPDFG KLYQEIDTAW RNSDAEGHHH HHH

Formula weight

17024.09 Da

Source organism

Neisseria meningitidis

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.8 %, Completeness: 93.0 %, Completeness (bb): 93.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.0 % (1661 of 1786)	93.1 % (860 of 924)	92.6 % (652 of 704)	94.3 % (149 of 158)
Backbone	93.8 % (842 of 898)	94.1 % (289 of 307)	93.5 % (419 of 448)	93.7 % (134 of 143)
Sidechain	92.4 % (952 of 1030)	92.5 % (571 of 617)	92.0 % (366 of 398)	100.0 % (15 of 15)
Aromatic	81.5 % (145 of 178)	82.0 % (73 of 89)	80.5 % (70 of 87)	100.0 % (2 of 2)
Methyl	97.5 % (156 of 160)	97.5 % (78 of 80)	97.5 % (78 of 80)

1. putative thioredoxin

MSLDSKTAPA FSLPDLHGKT VSNADLQGKV TLINFWFPSC PGCVSEMPKI IKTANDYKNK NFQVLAVAQP IDPIESVRQY VKDYGLPFTV MYDADKAVGQ AFGTQVYPTS VLIGKKGEIL KTYVGEPDFG KLYQEIDTAW RNSDAEGHHH HHH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pD6.6, 1mM DTT

#	Name	Isotope labeling	Concentration
7	putative thioredoxin	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	D20	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: 0.16 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: 0.16 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: -0.09 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: 0.17 ppm, Outliers: 3 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L5O, Strand ID: A Detail

Release date

2010-11-14

Citation

Solution structure and backbone dynamics of the cysteine 103 to serine mutant of the N-terminal domain of DsbD from Neisseria meningitidis
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.
Biochemistry (2008), 47, 12710-12720, PubMed 18983169 , DOI 10.1021/bi801343c , Abstract

Related entities 1. putative thioredoxin, : 1 : 99 entities Detail

Experiments performed 12 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	natural abundance	10 %

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pD6.6, 1mM DTT

#	Name	Isotope labeling	Concentration
7	putative thioredoxin	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pD6.6, 1mM DTT

#	Name	Isotope labeling	Concentration
7	putative thioredoxin	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pD6.6, 1mM DTT

#	Name	Isotope labeling	Concentration
7	putative thioredoxin	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pD6.6, 1mM DTT

#	Name	Isotope labeling	Concentration
7	putative thioredoxin	natural abundance	1 mM
8	sodium phosphate	natural abundance	20 mM
9	sodium chloride	natural abundance	100 mM
10	DTT	natural abundance	1 mM
11	D20	natural abundance	100 %

7 HNCO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	natural abundance	10 %

8 HNCACO

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	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 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	natural abundance	10 %

11 HNCACB

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	natural abundance	10 %

12 CBCACONH

Instrument

Bruker Avance - 500 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.0, Details 20mM Na phosphate buffer, 100mM NaCl, pH 7.0, 1mM DTT

#	Name	Isotope labeling	Concentration
1	putative thioredoxin	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	100 mM
4	DTT	natural abundance	1 mM
5	H20	natural abundance	90 %
6	D20	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_17277_2l5o.nef
Input source #2: Coordindates	2l5o.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-------
MSLDSKTAPAFSLPDLHGKTVSNADLQGKVTLINFWFPSCPGCVSEMPKIIKTANDYKNKNFQVLAVAQPIDPIESVRQYVKDYGLPFTVMYDADKAVGQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLDSKTAPAFSLPDLHGKTVSNADLQGKVTLINFWFPSCPGCVSEMPKIIKTANDYKNKNFQVLAVAQPIDPIESVRQYVKDYGLPFTVMYDADKAVGQ
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

100-------110-------120-------130-------140-------150
AFGTQVYPTSVLIGKKGEILKTYVGEPDFGKLYQEIDTAWRNSDAEGHHHHHH
|||||||||||||||||||||||||||||||||||||||||||||||||||||
AFGTQVYPTSVLIGKKGEILKTYVGEPDFGKLYQEIDTAWRNSDAEGHHHHHH
-------110-------120-------130-------140-------150---

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	153	0	0	100.0

Content subtype: combined_17277_2l5o.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1660		94.1 (chain: A, length: 153)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1975 (1)	noe	92.8 (chain: A, length: 153)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	92 (1)	noe	35.9 (chain: A, length: 153)
3	Distance restraints	CNS/XPLOR_distance_constraints_4	OK	90 (1)	hbond	40.5 (chain: A, length: 153)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_5	OK	194 (194)	.	76.5 (chain: A, length: 153)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 94.1%
- Total number of assignments
  - ¹H chemical shifts: 861
  - ¹³C chemical shifts: 650
  - ¹⁵N chemical shifts: 149
- 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	924	861	93.2
¹³C chemical shifts	704	650	92.3
¹⁵N chemical shifts	160	149	93.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	307	289	94.1
¹³C chemical shifts	306	285	93.1
¹⁵N chemical shifts	143	134	93.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	617	572	92.7
¹³C chemical shifts	398	365	91.7
¹⁵N chemical shifts	17	15	88.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	83	80	96.4
¹³C chemical shifts	83	80	96.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	89	71	79.8
¹³C chemical shifts	87	69	79.3
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: 153, Sequence coverage: 92.8%
- Total number of restraints: 1971
- Weight of restraints: 1.0 (1971)
- Potential type of restraints: square-well-parabolic (1971)
- 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_3
  - Status: OK
  - Experiment type: noe
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 153, Sequence coverage: 35.9%
  - Total number of restraints: 92
  - Weight of restraints: 1.0 (92)
  - Potential type of restraints: square-well-parabolic (92)
  - Range of distance target values: 2.65, 3.9 (Å)
  - Histogram of 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: 153, Sequence coverage: 40.5%
    - Total number of restraints: 90
    - Weight of restraints: 1.0 (90)
    - Potential type of restraints: square-well-parabolic (90)
    - 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: 153, Sequence coverage: 76.5%
- Total number of restraints: 194
- Total number of restraints per polymer type: 194
- Weight of restraints: 1.0 (194)
- Potential type of restraints: square-well-parabolic (194)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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

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Found 1 Document (0.799 seconds)

BMRB: 17277

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. putative thioredoxin, : 1 : 99 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail