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BMRB: 16731

2KUC

Solution Structure of a putative disulphide-isomerase from Bacteroides thetaiotaomicron

Authors

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

Assembly

putative disulphide-isomerase

Entity

1. putative disulphide-isomerase (polymer, Thiol state: all free), 130 monomers, 14801.89 Da Detail

MSLAQADGIA FRELSFPEAL KRAEVEDKLL FVDCFTTWCG PCKRLSKVVF KDSLVADYFN RHFVNLKMDM EKGEGVELRK KYGVHAYPTL LFINSSGEVV YRLVGAEDAP ELLKKVKLGV ESEGHHHHHH

Formula weight

14801.89 Da

Source organism

Bacteroides thetaiotaomicron

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 93.8 %, Completeness: 91.4 %, Completeness (bb): 91.7 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.4 % (1412 of 1545)	91.4 % (732 of 801)	91.5 % (561 of 613)	90.8 % (119 of 131)
Backbone	91.7 % (708 of 772)	92.1 % (244 of 265)	91.9 % (350 of 381)	90.5 % (114 of 126)
Sidechain	91.3 % (816 of 894)	91.2 % (489 of 536)	91.2 % (322 of 353)	100.0 % (5 of 5)
Aromatic	85.9 % (134 of 156)	87.2 % (68 of 78)	84.4 % (65 of 77)	100.0 % (1 of 1)
Methyl	97.2 % (140 of 144)	97.2 % (70 of 72)	97.2 % (70 of 72)

1. putative disulphide-isomerase

MSLAQADGIA FRELSFPEAL KRAEVEDKLL FVDCFTTWCG PCKRLSKVVF KDSLVADYFN RHFVNLKMDM EKGEGVELRK KYGVHAYPTL LFINSSGEVV YRLVGAEDAP ELLKKVKLGV ESEGHHHHHH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pH 7.5

#	Name	Isotope labeling	Concentration
1	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pD7.1

#	Name	Isotope labeling	Concentration
6	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	20 mM
9	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: 0.02 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: 0.02 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: 0.0 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: -0.03 ppm, Outliers: 2 Detail

Protein Blocks Logo

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

Release date

2010-03-21

Related entities 1. putative disulphide-isomerase, : 1 : 22 entities Detail

Experiments performed 6 experiments Detail

1 15N HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pH 7.5

#	Name	Isotope labeling	Concentration
1	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pH 7.5

#	Name	Isotope labeling	Concentration
1	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
2	sodium chloride	natural abundance	150 mM
3	sodium phosphate	natural abundance	20 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pD7.1

#	Name	Isotope labeling	Concentration
6	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	20 mM
9	D2O	natural abundance	100 %

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pD7.1

#	Name	Isotope labeling	Concentration
6	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	20 mM
9	D2O	natural abundance	100 %

5 13C NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pD7.1

#	Name	Isotope labeling	Concentration
6	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	20 mM
9	D2O	natural abundance	100 %

6 aromatic 13C NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1.0 atm, Temperature 298 K, pH 7.5, Details 20mM Na phosphate buffer, 150mM NaCl, pD7.1

#	Name	Isotope labeling	Concentration
6	putative disulphide-isomerase	[U-13C; U-15N]	1 mM
7	sodium chloride	natural abundance	150 mM
8	sodium phosphate	natural abundance	20 mM
9	D2O	natural abundance	100 %

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_16731_2kuc.nef
Input source #2: Coordindates	2kuc.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-------
MSLAQADGIAFRELSFPEALKRAEVEDKLLFVDCFTTWCGPCKRLSKVVFKDSLVADYFNRHFVNLKMDMEKGEGVELRKKYGVHAYPTLLFINSSGEVV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLAQADGIAFRELSFPEALKRAEVEDKLLFVDCFTTWCGPCKRLSKVVFKDSLVADYFNRHFVNLKMDMEKGEGVELRKKYGVHAYPTLLFINSSGEVV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

100-------110-------120-------
YRLVGAEDAPELLKKVKLGVESEGHHHHHH
||||||||||||||||||||||||||||||
YRLVGAEDAPELLKKVKLGVESEGHHHHHH
-------110-------120-------130

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	130	0	0	100.0

Content subtype: combined_16731_2kuc.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1417		93.1 (chain: A, length: 130)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2916 (1)	noe	92.3 (chain: A, length: 130)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	153 (1)	noe	46.2 (chain: A, length: 130)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	64 (1)	hbond	39.2 (chain: A, length: 130)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	177 (177)	.	84.6 (chain: A, length: 130)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 93.1%
- Total number of assignments
  - ¹H chemical shifts: 735
  - ¹³C chemical shifts: 565
  - ¹⁵N chemical shifts: 117
- 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

Comp_index_ID	Comp_ID	Atom_ID	CS value (ppm)
86	THR	HG1	5.49

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	801	734	91.6
¹³C chemical shifts	613	565	92.2
¹⁵N chemical shifts	137	117	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	265	242	91.3
¹³C chemical shifts	260	240	92.3
¹⁵N chemical shifts	126	112	88.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	536	492	91.8
¹³C chemical shifts	353	325	92.1
¹⁵N chemical shifts	11	5	45.5

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	75	72	96.0
¹³C chemical shifts	75	72	96.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	78	66	84.6
¹³C chemical shifts	77	65	84.4
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: 130, Sequence coverage: 92.3%
- Total number of restraints: 2900
- Weight of restraints: 1.0 (2900)
- Potential type of restraints: square-well-parabolic (2900)
- Range of distance target values: 2.4, 4.9 (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: 130, Sequence coverage: 46.2%
  - Total number of restraints: 153
  - Weight of restraints: 1.0 (153)
  - Potential type of restraints: square-well-parabolic (153)
  - 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_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 130, Sequence coverage: 39.2%
    - Total number of restraints: 64
    - Weight of restraints: 1.0 (64)
    - Potential type of restraints: square-well-parabolic (64)
    - 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: 130, Sequence coverage: 84.6%
- Total number of restraints: 177
- Total number of restraints per polymer type: 177
- Weight of restraints: 1.0 (177)
- Potential type of restraints: square-well-parabolic (177)
- 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, putative disulphide-isomerase, structural genomics, thioredoxin fold

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Found 1 Document (0.688 seconds)

BMRB: 16731

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. putative disulphide-isomerase, : 1 : 22 entities Detail

Experiments performed 6 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 6 contents Detail