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Found 1 Document (0.689 seconds)

BMRB: 17267

2L57

Solution Structure of an Uncharacterized Thioredoin-like Protein from Clostridium perfringens

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

uncharacterized thiredoxin-like protein

Entity

1. uncharacterized thiredoxin-like protein (polymer, Thiol state: all free), 126 monomers, 14717.59 Da Detail

MSLEGIKQIN FQSINVVENL EEAKEGIPTI IMFKTDTCPY CVEMQKELSY VSKEREGKFN IYYARLEEEK NIDLAYKYDA NIVPTTVFLD KEGNKFYVHQ GLMRKNNIET ILNSLGVKEG HHHHHH

Formula weight

14717.59 Da

Source organism

Clostridium perfringens

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 94.4 %, Completeness: 92.8 %, Completeness (bb): 92.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	92.8 % (1424 of 1534)	93.0 % (746 of 802)	92.4 % (550 of 595)	93.4 % (128 of 137)
Backbone	92.4 % (693 of 750)	91.4 % (234 of 256)	93.0 % (345 of 371)	92.7 % (114 of 123)
Sidechain	93.2 % (842 of 903)	93.8 % (512 of 546)	92.1 % (316 of 343)	100.0 % (14 of 14)
Aromatic	77.6 % (104 of 134)	80.6 % (54 of 67)	74.6 % (50 of 67)
Methyl	98.5 % (130 of 132)	98.5 % (65 of 66)	98.5 % (65 of 66)

1. uncharacterized thiredoxin-like protein

MSLEGIKQIN FQSINVVENL EEAKEGIPTI IMFKTDTCPY CVEMQKELSY VSKEREGKFN IYYARLEEEK NIDLAYKYDA NIVPTTVFLD KEGNKFYVHQ GLMRKNNIET ILNSLGVKEG 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 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	uncharacterized thiredoxin-like protein	[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	null	indirect	0.2514495
¹H	DSS	methyl protons	internal	direct	1.0
¹⁵N	DSS	methyl protons	null	indirect	0.1013291

Referencing offset: -0.01 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: -0.01 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: -0.1 ppm, Outliers: 3 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: 0.16 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2L57, Strand ID: A Detail

Release date

2010-11-07

Related entities 1. uncharacterized thiredoxin-like protein, : 1 : 15 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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 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	uncharacterized thiredoxin-like protein	[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	uncharacterized thiredoxin-like protein	[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

Bruker Avance - 800 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	uncharacterized thiredoxin-like protein	[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

Bruker Avance - 800 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	uncharacterized thiredoxin-like protein	[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

Varian Inova - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

8 HNCACO

Instrument

Bruker Avance - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

9 HNCA

Instrument

Bruker Avance - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

10 HNCOCA

Instrument

Bruker Avance - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

11 HNCACB

Instrument

Varian Inova - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 mM
5	H2O	natural abundance	90 %
6	D2O	natural abundance	10 %

12 CBCACONH

Instrument

Varian Inova - 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	uncharacterized thiredoxin-like protein	[U-100% 13C; U-100% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	DTT	natural abundance	1 mM
4	sodium chloride	natural abundance	50 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_17267_2l57.nef
Input source #2: Coordindates	2l57.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
MSLEGIKQINFQSINVVENLEEAKEGIPTIIMFKTDTCPYCVEMQKELSYVSKEREGKFNIYYARLEEEKNIDLAYKYDANIVPTTVFLDKEGNKFYVHQ
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLEGIKQINFQSINVVENLEEAKEGIPTIIMFKTDTCPYCVEMQKELSYVSKEREGKFNIYYARLEEEKNIDLAYKYDANIVPTTVFLDKEGNKFYVHQ

-------110-------120------
GLMRKNNIETILNSLGVKEGHHHHHH
||||||||||||||||||||||||||
GLMRKNNIETILNSLGVKEGHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	126	0	0	100.0

Content subtype: combined_17267_2l57.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1434		94.4 (chain: A, length: 126)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2075 (1)	noe	93.7 (chain: A, length: 126)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	92 (1)	noe	39.7 (chain: A, length: 126)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	74 (1)	hbond	42.9 (chain: A, length: 126)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	138 (138)	.	70.6 (chain: A, length: 126)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 94.4%
- Total number of assignments
  - ¹H chemical shifts: 753
  - ¹³C chemical shifts: 552
  - ¹⁵N chemical shifts: 129
- 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	802	753	93.9
¹³C chemical shifts	595	552	92.8
¹⁵N chemical shifts	140	129	92.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	256	239	93.4
¹³C chemical shifts	252	236	93.7
¹⁵N chemical shifts	123	113	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	546	514	94.1
¹³C chemical shifts	343	316	92.1
¹⁵N chemical shifts	17	16	94.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	70	69	98.6
¹³C chemical shifts	70	69	98.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	67	53	79.1
¹³C chemical shifts	67	49	73.1

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 93.7%
- Total number of restraints: 2068
- Weight of restraints: 1.0 (2068)
- Potential type of restraints: square-well-parabolic (2068)
- Range of distance target values: 2.4, 4.4 (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: 126, Sequence coverage: 39.7%
  - Total number of restraints: 91
  - Weight of restraints: 1.0 (91)
  - Potential type of restraints: square-well-parabolic (91)
  - Range of distance target values: 2.9, 4.15 (Å)
  - Histogram of distance target values
  - Distance restraints per residue
    - Chain_ID: A
  - Distance restraints on contact map
  - Saveframe: CNS/XPLOR_distance_constraints_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 42.9%
    - 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_4
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 126, Sequence coverage: 70.6%
- Total number of restraints: 138
- Total number of restraints per polymer type: 138
- Weight of restraints: 1.0 (138)
- Potential type of restraints: square-well-parabolic (138)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

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

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Found 1 Document (0.689 seconds)

BMRB: 17267

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. uncharacterized thiredoxin-like protein, : 1 : 15 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail