BMRBj - BMREntryMaster

Found 1 Document (0.702 seconds)

BMRB: 25464

2MYY

Solution structure of an MbtH-like protein from Mycobacterium marinum. Seattle Structural Genomics Center for Infectious Disease target MymaA.01649.c

Authors

Buchko, G.W.

Assembly

MbtH-like protein from Mycobacterium marinum

Entity

1. MbtH-like protein from Mycobacterium marinum (polymer, Thiol state: all free), 80 monomers, 9002.892 Da Detail

GPGSMKIMSD NPFDDEDGMF FVLINDEEQH SLWPTFADVP AGWRVVFGEA SRASCVEYVD QHWTDIRPKS LREKLASGQG

Formula weight

9002.892 Da

Source organism

Mycobacterium marinum ATCC BAA-535

Exptl. method

solution NMR

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 86.3 %, Completeness: 76.2 %, Completeness (bb): 79.8 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	76.2 % (699 of 917)	75.2 % (358 of 476)	76.5 % (274 of 358)	80.7 % (67 of 83)
Backbone	79.8 % (375 of 470)	80.2 % (130 of 162)	79.0 % (184 of 233)	81.3 % (61 of 75)
Sidechain	74.4 % (387 of 520)	72.6 % (228 of 314)	77.3 % (153 of 198)	75.0 % (6 of 8)
Aromatic	72.5 % (74 of 102)	72.5 % (37 of 51)	70.8 % (34 of 48)	100.0 % (3 of 3)
Methyl	87.9 % (58 of 66)	87.9 % (29 of 33)	87.9 % (29 of 33)

1. entity

GPGSMKIMSD NPFDDEDGMF FVLINDEEQH SLWPTFADVP AGWRVVFGEA SRASCVEYVD QHWTDIRPKS LREKLASGQG

Show sample condition

Sample #1

Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

Sample #2

Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
7	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
8	sodium chloride	natural abundance	100 (±2.0) mM
9	TRIS	natural abundance	20 (±0.5) mM
10	DTT	natural abundance	1 (±0.1) mM
11	D2O	natural abundance	100 %

LACS Plot; CA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 3 Detail

LACS Plot; CB

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: -0.05 ppm, Outliers: 3 Detail

LACS Plot; HA

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.03 ppm, Outliers: 5 Detail

LACS Plot; CO

Atom type	Mol. common name	Atom group	Ref. method	Ref. type	Shift ratio
¹H	DSS	methyl protons	internal	direct	1.0
¹³C	DSS	methyl protons	na	indirect	0.2514495
¹⁵N	DSS	methyl protons	na	indirect	0.1013291

Referencing offset: 0.05 ppm, Outliers: 1 Detail

Protein Blocks Logo

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

Release date

2015-03-29

Citation

Structural characterization of a β-hydroxyacid dehydrogenase from Geobacter sulfurreducens and Geobacter metallireducens with succinic semialdehyde reductase activity
Zhang, Y., Zheng, Y., Qin, L., Wang, S., Buchko, G.W., Garavito, R.
Biochimie (2014), 104, 61-69, PubMed 24878278 , DOI 10.1016/j.biochi.2014.05.002 , Abstract

Related entities 1. MbtH-like protein from Mycobacterium marinum, : 1 : 20 entities Detail

Experiments performed 11 experiments Detail

1 3D 1H-13C NOESY aliphatic

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

2 3D 1H-13C NOESY aromatic

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

3 3D 1H-15N NOESY

Instrument

Agilent VNMRS - 800 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

4 3D C(CO)NH

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

5 3D HNCO

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

6 3D HNCACB

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

7 2D 1H-15N HSQC

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

8 D2O exchange

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 100% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
7	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
8	sodium chloride	natural abundance	100 (±2.0) mM
9	TRIS	natural abundance	20 (±0.5) mM
10	DTT	natural abundance	1 (±0.1) mM
11	D2O	natural abundance	100 %

9 HBCBCGCDHD

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

10 2D 1H-13C HSQC aliphatic

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

11 2D 1H-13C HSQC aromatic

Instrument

Agilent VNMRS - 600 MHz

Sample

State isotropic, Solvent system 93% H2O/7% D2O, Pressure 1 atm, Temperature 293 K, pH 7

#	Name	Isotope labeling	Concentration
1	entity	[U-99% 13C; U-99% 15N]	1 (±0.2) mM
2	sodium chloride	natural abundance	100 (±2.0) mM
3	TRIS	natural abundance	20 (±0.5) mM
4	DTT	natural abundance	1 (±0.1) mM
5	D2O	natural abundance	7 %
6	H2O	natural abundance	93 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25464_2myy.nef
Input source #2: Coordindates	2myy.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
GPGSMKIMSDNPFDDEDGMFFVLINDEEQHSLWPTFADVPAGWRVVFGEASRASCVEYVDQHWTDIRPKSLREKLASGQG
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
GPGSMKIMSDNPFDDEDGMFFVLINDEEQHSLWPTFADVPAGWRVVFGEASRASCVEYVDQHWTDIRPKSLREKLASGQG

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	80	0	0	100.0

Content subtype: combined_25464_2myy.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	684		86.3 (chain: A, length: 80)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	1072 (1)	noe	78.7 (chain: A, length: 80)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	Warning	30 (1)	hbond	26.3 (chain: A, length: 80)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	86 (86)	.	67.5 (chain: A, length: 80)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 86.3%
- Total number of assignments
  - ¹H chemical shifts: 352
  - ¹³C chemical shifts: 267
  - ¹⁵N chemical shifts: 65
- 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	476	352	73.9
¹³C chemical shifts	358	267	74.6
¹⁵N chemical shifts	87	65	74.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	162	128	79.0
¹³C chemical shifts	160	117	73.1
¹⁵N chemical shifts	75	59	78.7

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	314	224	71.3
¹³C chemical shifts	198	150	75.8
¹⁵N chemical shifts	12	6	50.0

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	36	30	83.3
¹³C chemical shifts	36	30	83.3

Atom group	# of target shifts	# of assigned shifts	Completeness (%)
¹H chemical shifts	51	36	70.6
¹³C chemical shifts	48	32	66.7
¹⁵N chemical shifts	3	3	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: 80, Sequence coverage: 78.7%
- Total number of restraints: 1072
- Weight of restraints: 1.0 (1072)
- Potential type of restraints: square-well-parabolic (1072)
- Range of distance target values: 2.02, 3.65 (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: Warning
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 80, Sequence coverage: 26.3%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 1.9, 2.85 (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: 80, Sequence coverage: 67.5%
- Total number of restraints: 86
- Total number of restraints per polymer type: 86
- Weight of restraints: 1.0 (86)
- Potential type of restraints: square-well-parabolic (86)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords infectious diseases, tuberculosis, siderophore assembly, mycobactin

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Found 1 Document (0.702 seconds)

BMRB: 25464

Sample #1

Sample #2

Chemical shift reference

Chemical shift reference

Chemical shift reference

Chemical shift reference

Related entities 1. MbtH-like protein from Mycobacterium marinum, : 1 : 20 entities Detail

Experiments performed 11 experiments Detail

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NMR combined restraints 5 contents Detail