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Found 1 Document (1.08 seconds)

BMRB: 18387

2LRN

Solution structure of a thiol:disulfide interchange protein from Bacteroides sp.

Authors

Harris, R., Bandaranayake, A.D., Banu, R., Bonanno, J.B., Calarese, D.A., Celikgil, A., Chamala, S., Chan, M.K., Chaparro, R., Evans, B., Garforth, S., Gizzi, A., Hillerich, B., Kar, A., Lafleur, J., Lim, S., Love, J., Matikainen, B., Patel, H., Seidel, R.D., Smith, B., Stead, M., Girvin, M.E., Almo, S.C.

Assembly

thiol:disulfide interchange protein

Entity

1. thiol:disulfide interchange protein (polymer), 152 monomers, 17337.43 Da Detail

MSLATGSVAP AITGIDLKGN SVSLNDFKGK YVLVDFWFAG CSWCRKETPY LLKTYNAFKD KGFTIYGVST DRREEDWKKA IEEDKSYWNQ VLLQKDDVKD VLESYCIVGF PHIILVDPEG KIVAKELRGD DLYNTVEKFV NGAKEGHHHH HH

Formula weight

17337.43 Da

Source organism

Bacteroides sp.

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 93.2 %, Completeness (bb): 95.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1682 of 1805)	91.6 % (855 of 933)	94.9 % (676 of 712)	94.4 % (151 of 160)
Backbone	95.0 % (859 of 904)	93.3 % (291 of 312)	96.4 % (428 of 444)	94.6 % (140 of 148)
Sidechain	92.0 % (958 of 1041)	90.8 % (564 of 621)	93.9 % (383 of 408)	91.7 % (11 of 12)
Aromatic	85.6 % (173 of 202)	86.1 % (87 of 101)	84.5 % (82 of 97)	100.0 % (4 of 4)
Methyl	98.8 % (160 of 162)	97.5 % (79 of 81)	100.0 % (81 of 81)

1. thiol:disulfide interchange protein

MSLATGSVAP AITGIDLKGN SVSLNDFKGK YVLVDFWFAG CSWCRKETPY LLKTYNAFKD KGFTIYGVST DRREEDWKKA IEEDKSYWNQ VLLQKDDVKD VLESYCIVGF PHIILVDPEG KIVAKELRGD DLYNTVEKFV NGAKEGHHHH HH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.6, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
6	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	1 mM

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: -0.2 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: -0.2 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: -0.12 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: -0.13 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-05-20

Related entities 1. thiol:disulfide interchange protein, : 1 : 1 : 72 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 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

2 15N NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

3 13C CT-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.6, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
6	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	1 mM

4 aromatic 13C HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.6, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
6	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	1 mM

5 13C NOESY-HSQC

Instrument

Bruker Avance - 900 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.6, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
6	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	1 mM

6 13C aromatic NOESY-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.6, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
6	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
7	sodium phosphate	natural abundance	20 mM
8	sodium chloride	natural abundance	50 mM
9	DTT	natural abundance	1 mM
10	EDTA	natural abundance	1 mM

7 HNCO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

8 HNCACO

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

9 HNCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

10 HNCOCA

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

11 HNCACB

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

12 CBCACONH

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 7.0, Details 20mM Na phosphate buffer, 50mM NaCl, pH 7.0, 1mM DTT, 1mM EDTA

#	Name	Isotope labeling	Concentration
1	thiol:disulfide interchange protein	[U-13C; U-15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	EDTA	natural abundance	1 mM

NMR combined restraints 6 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18387_2lrn.nef
Input source #2: Coordindates	2lrn.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
MSLATGSVAPAITGIDLKGNSVSLNDFKGKYVLVDFWFAGCSWCRKETPYLLKTYNAFKDKGFTIYGVSTDRREEDWKKAIEEDKSYWNQVLLQKDDVKD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLATGSVAPAITGIDLKGNSVSLNDFKGKYVLVDFWFAGCSWCRKETPYLLKTYNAFKDKGFTIYGVSTDRREEDWKKAIEEDKSYWNQVLLQKDDVKD

-------110-------120-------130-------140-------150--
VLESYCIVGFPHIILVDPEGKIVAKELRGDDLYNTVEKFVNGAKEGHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||
VLESYCIVGFPHIILVDPEGKIVAKELRGDDLYNTVEKFVNGAKEGHHHHHH

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	152	0	0	100.0

Content subtype: combined_18387_2lrn.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1699		96.7 (chain: A, length: 152)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3268 (1)	noe	96.1 (chain: A, length: 152)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	424 (1)	noe	71.7 (chain: A, length: 152)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	106 (1)	hbond	50.0 (chain: A, length: 152)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	186 (186)	.	76.3 (chain: A, length: 152)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 152, Sequence coverage: 96.7%
- Total number of assignments
  - ¹H chemical shifts: 874
  - ¹³C chemical shifts: 676
  - ¹⁵N chemical shifts: 149
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- Peptide bond of PRO
- 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	933	874	93.7
¹³C chemical shifts	712	676	94.9
¹⁵N chemical shifts	164	149	90.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	312	294	94.2
¹³C chemical shifts	304	292	96.1
¹⁵N chemical shifts	148	137	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	621	580	93.4
¹³C chemical shifts	408	384	94.1
¹⁵N chemical shifts	16	12	75.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	82	81	98.8
¹³C chemical shifts	82	81	98.8

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	101	86	85.1
¹³C chemical shifts	97	82	84.5
¹⁵N chemical shifts	4	4	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: 152, Sequence coverage: 96.1%
- Total number of restraints: 3262
- Weight of restraints: 1.0 (3262)
- Potential type of restraints: square-well-parabolic (3262)
- Range of distance target values: 2.1, 5.6 (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: 152, Sequence coverage: 71.7%
  - Total number of restraints: 418
  - Weight of restraints: 1.0 (418)
  - Potential type of restraints: square-well-parabolic (418)
  - Range of distance target values: 2.35, 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_5
    - Status: OK
    - Experiment type: hbond
    - Sequence coverage of experimental data
      - Entity_assembly_ID: A, Chain length: 152, Sequence coverage: 50.0%
    - Total number of restraints: 106
    - Weight of restraints: 1.0 (106)
    - Potential type of restraints: square-well-parabolic (106)
    - Range of distance target values: 1.7, 2.7 (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: 152, Sequence coverage: 76.3%
- Total number of restraints: 186
- Total number of restraints per polymer type: 186
- Weight of restraints: 1.0 (186)
- Potential type of restraints: square-well-parabolic (186)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords New York Structural Genomics Research Consortium, STRUCTURAL GENOMICS, THIOREDOXIN-LIKE

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Found 1 Document (1.08 seconds)

BMRB: 18387

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. thiol:disulfide interchange protein, : 1 : 1 : 72 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail