BMRBj - BMREntryMaster

Found 1 Document (0.755 seconds)

BMRB: 17811

2LGJ

Solution structure of MsPTH

Authors

Yadav, R., Pathak, P., Pulavarti, S., Jain, A., Kumar, A., Shukla, V., Arora, A.

Assembly

MsPTH

Entity

1. MsPTH (polymer, Thiol state: not present), 191 monomers, 20278.07 Da Detail

MAEPLLVVGL GNPGPTYAKT RHNLGFMVAD VLAGRIGSAF KVHKKSGAEV VTGRLAGTSV VLAKPRCYMN ESGRQVGPLA KFYSVPPQQI VVIHDELDID FGRIRLKLGG GEGGHNGLRS VASALGTKNF HRVRIGVGRP PGRKDPAAFV LENFTAAERA EVPTIVEQAA DATELLIAQG LEPAQNTVHA W

Formula weight

20278.07 Da

Source organism

Mycolicibacterium smegmatis

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 97.4 %, Completeness: 88.3 %, Completeness (bb): 96.0 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	88.3 % (1884 of 2134)	87.6 % (966 of 1103)	89.3 % (748 of 838)	88.1 % (170 of 193)
Backbone	96.0 % (1077 of 1122)	95.2 % (374 of 393)	97.1 % (534 of 550)	94.4 % (169 of 179)
Sidechain	82.2 % (970 of 1180)	83.4 % (592 of 710)	82.7 % (377 of 456)	7.1 % (1 of 14)
Aromatic	31.5 % (41 of 130)	32.3 % (21 of 65)	31.3 % (20 of 64)	0.0 % (0 of 1)
Methyl	97.5 % (236 of 242)	99.2 % (120 of 121)	95.9 % (116 of 121)

1. MsPTH

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MsPTH	[U-98% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	AEBSF protease inhibitor	natural abundance	1 mM
6	sodium azide	natural abundance	1 %
7	H2O	natural abundance	93 %
8	D2O	natural abundance	7 %

Sample #2

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	MsPTH	[U-98% 13C; U-98% 15N]	0.9 mM
18	sodium phosphate	natural abundance	20 mM
19	sodium chloride	natural abundance	50 mM
20	DTT	natural abundance	1 mM
21	AEBSF protease inhibitor	natural abundance	1 mM
22	sodium azide	natural abundance	1 %
23	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: -0.05 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: -0.05 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: 2 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: -0.12 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2012-08-29

Citation

Solution structure of MsPTH
Yadav, R., Pathak, P., Pulavarti, S., Jain, A., Kumar, A., Shukla, V., Arora, A.
J. Biol. Chem.

Related entities 1. MsPTH, : 1 : 2 : 201 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 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MsPTH	[U-98% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	AEBSF protease inhibitor	natural abundance	1 mM
6	sodium azide	natural abundance	1 %
7	H2O	natural abundance	93 %
8	D2O	natural abundance	7 %

2 3D HNCACB

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

4 3D HNCA

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

5 3D HNCO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

6 3D HN(CA)CO

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

7 3D H(CCO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

8 3D C(CO)NH

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
1	MsPTH	[U-98% 15N]	1 mM
2	sodium phosphate	natural abundance	20 mM
3	sodium chloride	natural abundance	50 mM
4	DTT	natural abundance	1 mM
5	AEBSF protease inhibitor	natural abundance	1 mM
6	sodium azide	natural abundance	1 %
7	H2O	natural abundance	93 %
8	D2O	natural abundance	7 %

11 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	MsPTH	[U-98% 13C; U-98% 15N]	0.9 mM
18	sodium phosphate	natural abundance	20 mM
19	sodium chloride	natural abundance	50 mM
20	DTT	natural abundance	1 mM
21	AEBSF protease inhibitor	natural abundance	1 mM
22	sodium azide	natural abundance	1 %
23	D2O	natural abundance	100 %

12 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	MsPTH	[U-98% 13C; U-98% 15N]	0.9 mM
18	sodium phosphate	natural abundance	20 mM
19	sodium chloride	natural abundance	50 mM
20	DTT	natural abundance	1 mM
21	AEBSF protease inhibitor	natural abundance	1 mM
22	sodium azide	natural abundance	1 %
23	D2O	natural abundance	100 %

13 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	MsPTH	[U-98% 13C; U-98% 15N]	0.9 mM
18	sodium phosphate	natural abundance	20 mM
19	sodium chloride	natural abundance	50 mM
20	DTT	natural abundance	1 mM
21	AEBSF protease inhibitor	natural abundance	1 mM
22	sodium azide	natural abundance	1 %
23	D2O	natural abundance	100 %

14 2D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
17	MsPTH	[U-98% 13C; U-98% 15N]	0.9 mM
18	sodium phosphate	natural abundance	20 mM
19	sodium chloride	natural abundance	50 mM
20	DTT	natural abundance	1 mM
21	AEBSF protease inhibitor	natural abundance	1 mM
22	sodium azide	natural abundance	1 %
23	D2O	natural abundance	100 %

15 HB(CBCGCE)HE

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

16 HB(CBCGCD)HD

Instrument

Varian INOVA - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 303 K, pH 6.5

#	Name	Isotope labeling	Concentration
9	MsPTH	[U-98% 13C; U-98% 15N]	1 mM
10	sodium phosphate	natural abundance	20 mM
11	sodium chloride	natural abundance	50 mM
12	DTT	natural abundance	1 mM
13	AEBSF protease inhibitor	natural abundance	1 mM
14	sodium azide	natural abundance	1 %
15	H2O	natural abundance	93 %
16	D2O	natural abundance	7 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_17811_2lgj.nef
Input source #2: Coordindates	2lgj.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
MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIGSAFKVHKKSGAEVVTGRLAGTSVVLAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDID
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MAEPLLVVGLGNPGPTYAKTRHNLGFMVADVLAGRIGSAFKVHKKSGAEVVTGRLAGTSVVLAKPRCYMNESGRQVGPLAKFYSVPPQQIVVIHDELDID

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

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	191	0	0	100.0

Content subtype: combined_17811_2lgj.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1849		96.3 (chain: A, length: 191)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	2637 (1)	noe	94.8 (chain: A, length: 191)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	277 (277)	.	93.7 (chain: A, length: 191)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 96.3%
- Total number of assignments
  - ¹H chemical shifts: 949
  - ¹³C chemical shifts: 735
  - ¹⁵N chemical shifts: 165
- 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	1103	949	86.0
¹³C chemical shifts	838	735	87.7
¹⁵N chemical shifts	206	165	80.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	393	371	94.4
¹³C chemical shifts	382	368	96.3
¹⁵N chemical shifts	179	165	92.2

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	710	578	81.4
¹³C chemical shifts	456	367	80.5
¹⁵N chemical shifts	27	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	124	122	98.4
¹³C chemical shifts	124	113	91.1

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	65	20	30.8
¹³C chemical shifts	64	20	31.2
¹⁵N chemical shifts	1	0	0.0

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 191, Sequence coverage: 94.8%
- Total number of restraints: 2566
- Weight of restraints: 1.0 (2566)
- Potential type of restraints: square-well-parabolic (2566)
- 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: 191, Sequence coverage: 93.7%
- Total number of restraints: 277
- Total number of restraints per polymer type: 277
- Weight of restraints: 1.0 (277)
- Potential type of restraints: square-well-parabolic (277)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MsPTH, NMR, Solution structure

Search

Query history

Resources

Search for primary databases

Search for subsidiary databases

Display

Hits per page

Statistics

Query Changes will take effect after "OK" button is selected.

Maximum hits

Default conjunction operator

Omni-box

Search filter

Sequence search (BLAST)

E-value

Query sequence coverage

Miscellaneous

The number of previewed publications

Completeness of assigned chemical shift

Sequence chart about top aligned regions

Sequence chart about interacting regions

Hit context with highlight

Link destinations for BMRB, PDB and EMDB

Found 1 Document (0.755 seconds)

BMRB: 17811

Sample #1

Sample #2

Sample #3

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MsPTH, : 1 : 2 : 201 entities Detail

Experiments performed 16 experiments Detail

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

Instrument

Sample

NMR combined restraints 4 contents Detail