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Found 1 Document (0.818 seconds)

BMRB: 19731

2MJL

Solution structure of peptidyl-tRNA hyrolase from Vibrio cholerae

Authors

Kabra, A., Shahid, S., Yadav, R., Pulavarti, S., Shukla, V.K., Arora, A.

Assembly

peptidyl-tRNA hyrolase from Vibrio cholerae

Entity

1. peptidyl-tRNA hyrolase from Vibrio cholerae (polymer), 197 monomers, 21581.73 Da Detail

MVSQPIKLLV GLANPGPEYA KTRHNAGAWV VEELARIHNV TLKNEPKFFG LTGRLLINSQ ELRVLIPTTF MNLSGKAIAA LANFYQIKPE EIMVAHDELD LPPGVAKFKQ GGGHGGHNGL KDTISKLGNN KEFYRLRLGI GHPGHKDKVA GYVLGKAPAK EQECLDAAVD ESVRCLEILM KDGLTKAQNR LHTFKAE

Formula weight

21581.73 Da

Source organism

Vibrio cholerae

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.0 %, Completeness: 91.1 %, Completeness (bb): 97.6 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	91.1 % (2097 of 2301)	89.7 % (1077 of 1201)	93.3 % (835 of 895)	90.2 % (185 of 205)
Backbone	97.6 % (1134 of 1162)	97.3 % (393 of 404)	97.7 % (558 of 571)	97.9 % (183 of 187)
Sidechain	86.4 % (1137 of 1316)	85.8 % (684 of 797)	90.0 % (451 of 501)	11.1 % (2 of 18)
Aromatic	71.2 % (104 of 146)	71.2 % (52 of 73)	72.2 % (52 of 72)	0.0 % (0 of 1)
Methyl	97.5 % (230 of 236)	99.2 % (117 of 118)	95.8 % (113 of 118)

1. VcPth

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	VcPth	[U-100% 15N]	0.9 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.1 %
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	93 %
14	D2O	natural abundance	7 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	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: -0.12 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: -0.12 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: -0.04 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: 0.01 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 10 models in PDB: 2MJL, Strand ID: A Detail

Release date

2015-01-19

Citation

Solution structure of peptidyl-tRNA hydrolase from Vibrio cholerae
Kabra, A., Shahid, S., Yadav, R., Pulavarti, S., Shukla, V.K., Arora, A.
Not known

Related entities 1. peptidyl-tRNA hyrolase from Vibrio cholerae, : 1 : 5 : 197 entities Detail

Experiments performed 16 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	VcPth	[U-100% 15N]	0.9 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.1 %
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	93 %
14	D2O	natural abundance	7 %

2 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

3 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

4 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

5 3D HNCACB

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

7 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

8 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

9 2D 1H-13C HSQC

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

10 2D 1H-13C HSQC aromatic

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

11 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
8	VcPth	[U-100% 15N]	0.9 mM
9	sodium phosphate	natural abundance	20 mM
10	sodium chloride	natural abundance	50 mM
11	sodium azide	natural abundance	0.1 %
12	DTT	natural abundance	1 mM
13	H2O	natural abundance	93 %
14	D2O	natural abundance	7 %

12 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

13 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

14 3D-HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	sodium azide	natural abundance	0.1 %
5	DTT	natural abundance	1 mM
6	H2O	natural abundance	93 %
7	D2O	natural abundance	7 %

15 2D-CBHE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

16 2D-CBHD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 273 K, pH 6.5

#	Name	Isotope labeling	Concentration
15	VcPth	[U-100% 13C; U-100% 15N]	0.9 mM
16	sodium phosphate	natural abundance	20 mM
17	sodium chloride	natural abundance	50 mM
18	sodium azide	natural abundance	0.1 %
19	DTT	natural abundance	1 mM
20	D2O	natural abundance	100 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19731_2mjl.nef
Input source #2: Coordindates	2mjl.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
MVSQPIKLLVGLANPGPEYAKTRHNAGAWVVEELARIHNVTLKNEPKFFGLTGRLLINSQELRVLIPTTFMNLSGKAIAALANFYQIKPEEIMVAHDELD
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MVSQPIKLLVGLANPGPEYAKTRHNAGAWVVEELARIHNVTLKNEPKFFGLTGRLLINSQELRVLIPTTFMNLSGKAIAALANFYQIKPEEIMVAHDELD

-------110-------120-------130-------140-------150-------160-------170-------180-------190-------
LPPGVAKFKQGGGHGGHNGLKDTISKLGNNKEFYRLRLGIGHPGHKDKVAGYVLGKAPAKEQECLDAAVDESVRCLEILMKDGLTKAQNRLHTFKAE
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LPPGVAKFKQGGGHGGHNGLKDTISKLGNNKEFYRLRLGIGHPGHKDKVAGYVLGKAPAKEQECLDAAVDESVRCLEILMKDGLTKAQNRLHTFKAE

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	197	0	0	100.0

Content subtype: combined_19731_2mjl.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	2061		98.0 (chain: A, length: 197)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	3384 (1)	noe	95.9 (chain: A, length: 197)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	328 (328)	.	95.9 (chain: A, length: 197)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 197, Sequence coverage: 98.0%
- Total number of assignments
  - ¹H chemical shifts: 1053
  - ¹³C chemical shifts: 826
  - ¹⁵N chemical shifts: 182
- 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	1201	1052	87.6
¹³C chemical shifts	895	826	92.3
¹⁵N chemical shifts	213	182	85.4

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	404	393	97.3
¹³C chemical shifts	394	384	97.5
¹⁵N chemical shifts	187	182	97.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	797	659	82.7
¹³C chemical shifts	501	442	88.2
¹⁵N chemical shifts	26	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	122	117	95.9
¹³C chemical shifts	122	113	92.6

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	73	51	69.9
¹³C chemical shifts	72	50	69.4
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 197, Sequence coverage: 95.9%
- Total number of restraints: 3375
- Weight of restraints: 1.0 (3375)
- Potential type of restraints: square-well-parabolic (3375)
- Range of distance target values: 2.0, 3.25 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 197, Sequence coverage: 95.9%
- Total number of restraints: 328
- Total number of restraints per polymer type: 328
- Weight of restraints: 1.0 (328)
- Potential type of restraints: square-well-parabolic (328)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords VcPth

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Found 1 Document (0.818 seconds)

BMRB: 19731

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. peptidyl-tRNA hyrolase from Vibrio cholerae, : 1 : 5 : 197 entities Detail

Experiments performed 16 experiments Detail

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NMR combined restraints 4 contents Detail