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Found 1 Document (0.717 seconds)

BMRB: 18602

2LW3

Solution structure of the soluble domain of MmpS4 from Mycobacterium tuberculosis

Authors

Xi, Z., Sun, P., Wang, W., Lai, C., Wu, F., Tian, C.

Assembly

soluble domain of MmpS4

Entity

1. soluble domain of MmpS4 (polymer, Thiol state: all free), 90 monomers, 9717.788 Da Detail

MHLTYEIFGP PGTVADISYF DVNSEPQRVD GAVLPWSLHI TTNDAAVMGN IVAQGNSDSI GCRITVDGKV RAERVSNEVN AYTYCLVKSA

Formula weight

9717.788 Da

Source organism

Mycobacterium tuberculosis

Exptl. method

solution NMR

Refine. method

simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 95.6 %, Completeness: 75.9 %, Completeness (bb): 87.2 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	75.9 % (746 of 983)	73.2 % (366 of 500)	78.1 % (303 of 388)	81.1 % (77 of 95)
Backbone	87.2 % (464 of 532)	84.7 % (155 of 183)	88.2 % (232 of 263)	89.5 % (77 of 86)
Sidechain	67.4 % (360 of 534)	66.6 % (211 of 317)	71.6 % (149 of 208)	0.0 % (0 of 9)
Aromatic	2.8 % (2 of 72)	0.0 % (0 of 36)	5.7 % (2 of 35)	0.0 % (0 of 1)
Methyl	82.1 % (92 of 112)	82.1 % (46 of 56)	82.1 % (46 of 56)

1. soluble domain of MmpS4

MHLTYEIFGP PGTVADISYF DVNSEPQRVD GAVLPWSLHI TTNDAAVMGN IVAQGNSDSI GCRITVDGKV RAERVSNEVN AYTYCLVKSA

Show sample condition

Sample #1

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

Sample #2

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	MmpS4	[U-100% 15N]	0.2 ~ 0.5 mM
7	DTT	natural abundance	2 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

Sample #3

Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
11	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
12	DTT	natural abundance	2 mM
13	sodium phosphate	natural abundance	50 mM
14	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: -0.04 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: -0.04 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: -0.16 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: 0.86 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2LW3, Strand ID: A Detail

Release date

2013-03-10

Citation

Discovery of a siderophore export system essential for virulence of Mycobacterium tuberculosis
Wells, R.M., Jones, C.M., Xi, Z., Speer, A., Danilchanka, O., Doornbos, K.S., Sun, P., Wu, F., Tian, C., Niederweis, M.
PLoS Pathog. (2013), 9, e1003120-e1003120, PubMed 23431276 , DOI 10.1371/journal.ppat.1003120 , Abstract

Related entities 1. soluble domain of MmpS4, : 1 : 2 : 10 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	MmpS4	[U-100% 15N]	0.2 ~ 0.5 mM
7	DTT	natural abundance	2 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

2 2D 1H-13C HSQC

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

3 3D CBCA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

4 3D HNCO

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

5 3D HNCA

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

6 3D HNCACB

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

7 3D HBHA(CO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

8 3D H(CCO)NH

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

9 3D HCCH-TOCSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

10 3D 1H-15N NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
6	MmpS4	[U-100% 15N]	0.2 ~ 0.5 mM
7	DTT	natural abundance	2 mM
8	sodium phosphate	natural abundance	50 mM
9	H2O	natural abundance	90 %
10	D2O	natural abundance	10 %

11 3D 1H-13C NOESY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
11	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
12	DTT	natural abundance	2 mM
13	sodium phosphate	natural abundance	50 mM
14	D2O	natural abundance	100 %

12 3D HCCH-COSY

Instrument

Varian INOVA - 500 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.5

#	Name	Isotope labeling	Concentration
1	MmpS4	[U-100% 13C; U-100% 15N]	0.2 ~ 0.5 mM
2	DTT	natural abundance	2 mM
3	sodium phosphate	natural abundance	50 mM
4	H2O	natural abundance	90 %
5	D2O	natural abundance	10 %

NMR combined restraints 4 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_18602_2lw3.nef
Input source #2: Coordindates	2lw3.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

--------60--------70--------80--------90-------100-------110-------120-------130-------140
MHLTYEIFGPPGTVADISYFDVNSEPQRVDGAVLPWSLHITTNDAAVMGNIVAQGNSDSIGCRITVDGKVRAERVSNEVNAYTYCLVKSA
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MHLTYEIFGPPGTVADISYFDVNSEPQRVDGAVLPWSLHITTNDAAVMGNIVAQGNSDSIGCRITVDGKVRAERVSNEVNAYTYCLVKSA
--------10--------20--------30--------40--------50--------60--------70--------80--------90

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	90	0	0	100.0

Content subtype: combined_18602_2lw3.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	733		94.4 (chain: A, length: 90)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	961 (1)	noe	87.8 (chain: A, length: 90)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_3	OK	122 (122)	.	87.8 (chain: A, length: 90)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 94.4%
- Total number of assignments
  - ¹H chemical shifts: 363
  - ¹³C chemical shifts: 296
  - ¹⁵N chemical shifts: 74
- 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	500	363	72.6
¹³C chemical shifts	388	296	76.3
¹⁵N chemical shifts	99	74	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	183	161	88.0
¹³C chemical shifts	180	155	86.1
¹⁵N chemical shifts	86	74	86.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	317	202	63.7
¹³C chemical shifts	208	141	67.8
¹⁵N chemical shifts	13	0	0.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	58	45	77.6
¹³C chemical shifts	58	44	75.9

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	0	0.0
¹³C chemical shifts	35	0	0.0
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: 90, Sequence coverage: 87.8%
- Total number of restraints: 960
- Weight of restraints: 1.0 (960)
- Potential type of restraints: square-well-parabolic (960)
- Range of distance target values: 2.15, 3.9 (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

Dihedral angle restraints

Saveframe: CNS/XPLOR_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 87.8%
- Total number of restraints: 122
- Total number of restraints per polymer type: 122
- Weight of restraints: 1.0 (122)
- Potential type of restraints: square-well-parabolic (122)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords MmpS4, Mycobacterium tuberculosis, soluble domain, solution structure

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Found 1 Document (0.717 seconds)

BMRB: 18602

Sample #1

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Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. soluble domain of MmpS4, : 1 : 2 : 10 entities Detail

Experiments performed 12 experiments Detail

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NMR combined restraints 4 contents Detail