BMRBj - BMREntryMaster

Found 1 Document (0.635 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

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 (0.635 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

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 5 contents Detail