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Found 1 Document (1.357 seconds)

BMRB: 18394

2LRT

Solution structure of the uncharacterized thioredoxin-like protein BVU_1432 from Bacteroides vulgatus

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

uncharacterized thioredoxin-like protein BVU 1432

Entity

1. uncharacterized thioredoxin-like protein BVU 1432 (polymer, Thiol state: all free), 152 monomers, 17297.26 Da Detail

MSLEIPEDKI KEASIIDIQL KDLKGNTRSL TDLKGKVVLI DFTVYNNAMS AAHNLALREL YNKYASQGFE IYQISLDGDE HFWKTSADNL PWVCVRDANG AYSSYISLYN VTNLPSVFLV NRNNELSARG ENIKDLDEAI KKLLEGHHHH HH

Formula weight

17297.26 Da

Source organism

Phocaeicola vulgatus

Exptl. method

solution NMR

Refine. method

simulating annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 94.5 %, Completeness (bb): 94.9 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	94.5 % (1691 of 1789)	94.3 % (872 of 925)	94.7 % (660 of 697)	95.2 % (159 of 167)
Backbone	94.9 % (860 of 906)	94.5 % (291 of 308)	95.3 % (428 of 449)	94.6 % (141 of 149)
Sidechain	94.5 % (971 of 1028)	94.2 % (581 of 617)	94.7 % (372 of 393)	100.0 % (18 of 18)
Aromatic	82.9 % (126 of 152)	82.9 % (63 of 76)	82.4 % (61 of 74)	100.0 % (2 of 2)
Methyl	98.9 % (178 of 180)	97.8 % (88 of 90)	100.0 % (90 of 90)

1. uncharacterized thioredoxin-like protein

MSLEIPEDKI KEASIIDIQL KDLKGNTRSL TDLKGKVVLI DFTVYNNAMS AAHNLALREL YNKYASQGFE IYQISLDGDE HFWKTSADNL PWVCVRDANG AYSSYISLYN VTNLPSVFLV NRNNELSARG ENIKDLDEAI KKLLEGHHHH HH

Show sample condition

Sample #1

Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
6	uncharacterized thioredoxin-like 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: -0.1 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: -0.1 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: -0.05 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: 3 Detail

Protein Blocks Logo

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

Release date

2012-04-23

Related entities 1. uncharacterized thioredoxin-like protein BVU 1432, : 1 : 27 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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
6	uncharacterized thioredoxin-like 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 CT-HSQC

Instrument

Varian Inova - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
6	uncharacterized thioredoxin-like 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 - 700 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
6	uncharacterized thioredoxin-like 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 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pD6.4, 1mM DTT

#	Name	Isotope labeling	Concentration
6	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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

Bruker Avance - 700 MHz

Sample

State isotropic, Solvent system 90% H2O, 10% D2O, Pressure 1 atm, Temperature 303 K, pH 6.8, Details 20mM Na phosphate buffer, 50mM NaCl, pH 6.8, 1mM DTT

#	Name	Isotope labeling	Concentration
1	uncharacterized thioredoxin-like 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_18394_2lrt.nef
Input source #2: Coordindates	2lrt.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
MSLEIPEDKIKEASIIDIQLKDLKGNTRSLTDLKGKVVLIDFTVYNNAMSAAHNLALRELYNKYASQGFEIYQISLDGDEHFWKTSADNLPWVCVRDANG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MSLEIPEDKIKEASIIDIQLKDLKGNTRSLTDLKGKVVLIDFTVYNNAMSAAHNLALRELYNKYASQGFEIYQISLDGDEHFWKTSADNLPWVCVRDANG

-------110-------120-------130-------140-------150--
AYSSYISLYNVTNLPSVFLVNRNNELSARGENIKDLDEAIKKLLEGHHHHHH
||||||||||||||||||||||||||||||||||||||||||||||||||||
AYSSYISLYNVTNLPSVFLVNRNNELSARGENIKDLDEAIKKLLEGHHHHHH

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_18394_2lrt.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1694		96.7 (chain: A, length: 152)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	3509 (1)	noe	94.7 (chain: A, length: 152)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	163 (1)	noe	52.0 (chain: A, length: 152)
3	Distance restraints	CNS/XPLOR_distance_constraints_5	OK	86 (1)	hbond	40.8 (chain: A, length: 152)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	179 (179)	.	70.4 (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: 875
  - ¹³C chemical shifts: 662
  - ¹⁵N chemical shifts: 157
- 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	925	875	94.6
¹³C chemical shifts	697	662	95.0
¹⁵N chemical shifts	172	157	91.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	308	290	94.2
¹³C chemical shifts	304	291	95.7
¹⁵N chemical shifts	149	137	91.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	617	585	94.8
¹³C chemical shifts	393	371	94.4
¹⁵N chemical shifts	23	20	87.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	92	92	100.0
¹³C chemical shifts	92	92	100.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	76	63	82.9
¹³C chemical shifts	74	61	82.4
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: 152, Sequence coverage: 94.7%
- Total number of restraints: 3496
- Weight of restraints: 1.0 (3496)
- Potential type of restraints: square-well-parabolic (3496)
- 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: 152, Sequence coverage: 52.0%
  - Total number of restraints: 163
  - Weight of restraints: 1.0 (163)
  - Potential type of restraints: square-well-parabolic (163)
  - Range of distance target values: 2.4, 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: 152, Sequence coverage: 40.8%
    - Total number of restraints: 86
    - Weight of restraints: 1.0 (86)
    - Potential type of restraints: square-well-parabolic (86)
    - 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: 152, Sequence coverage: 70.4%
- Total number of restraints: 179
- Total number of restraints per polymer type: 179
- Weight of restraints: 1.0 (179)
- Potential type of restraints: square-well-parabolic (179)
- 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, UNKNOWN FUNCTION

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Found 1 Document (1.357 seconds)

BMRB: 18394

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. uncharacterized thioredoxin-like protein BVU 1432, : 1 : 27 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 6 contents Detail