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BMRB: 19755

2MK6

Structure determination of substrate binding domain of MecA

Authors

Zhang, Y., Zhang, Y., Jin, C., Shi, Y.

Assembly

MecA

Entity

1. MecA (polymer, Thiol state: not present), 90 monomers, 10891.07 Da Detail

MEIERINEHT VKFYMSYGDI EDRGFDREEI WYNRERSEEL FWEVMDEVHE EEEFAVEGPL WIQVQALDKG LEIIVTKAQL SKDLDKLVPR

Formula weight

10891.07 Da

Source organism

Bacillus subtilis subsp. spizizenii ATCC 6633 = JCM 2499

Exptl. method

Refine. method

molecular dynamics

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 100.0 %, Completeness: 93.2 %, Completeness (bb): 95.3 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	93.2 % (1034 of 1109)	91.7 % (533 of 581)	95.1 % (411 of 432)	93.8 % (90 of 96)
Backbone	95.3 % (511 of 536)	95.6 % (174 of 182)	95.9 % (255 of 266)	93.2 % (82 of 88)
Sidechain	92.4 % (609 of 659)	90.0 % (359 of 399)	96.0 % (242 of 252)	100.0 % (8 of 8)
Aromatic	90.7 % (98 of 108)	90.7 % (49 of 54)	90.2 % (46 of 51)	100.0 % (3 of 3)
Methyl	90.4 % (85 of 94)	89.4 % (42 of 47)	91.5 % (43 of 47)

1. MecA-NTD

MEIERINEHT VKFYMSYGDI EDRGFDREEI WYNRERSEEL FWEVMDEVHE EEEFAVEGPL WIQVQALDKG LEIIVTKAQL SKDLDKLVPR

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: -0.35 ppm, Outliers: 3 Detail

LACS Plot; CB

Referencing offset: -0.35 ppm, Outliers: 3 Detail

LACS Plot; HA

Referencing offset: -0.03 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.09 ppm, Outliers: 1 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MK6, Strand ID: A Detail

Release date

2015-02-08

Citation

NMR structure and interaction analysis of the substrate binding domain of MecA
Zhang, Y., Zhang, Y., Jin, C., Shi, Y.
Nat. Struct. Biol.

Related entities 1. MecA, : 1 : 5 : 55 entities Detail

Interaction partners 1. MecA, : 4 interactors Detail

More details for 4 interactors identified by 2 citations

Experiments performed 14 experiments Detail

1 2D 1H-15N HSQC

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

2 2D 1H-13C HSQC aliphatic

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

3 2D 1H-13C HSQC aromatic

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

4 3D HNCO

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

5 3D HNCA

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

6 3D HNCACB

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

7 3D HBHA(CO)NH

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

8 3D HN(CO)CA

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

9 3D HCCH-TOCSY

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

10 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

11 3D 1H-13C NOESY aliphatic

Instrument

Bruker Avance - 800 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

12 3D 1H-13C NOESY aromatic

Instrument

Bruker Avance - 800 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

13 3D HCCH-COSY

Instrument

Bruker Avance - 700 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	D2O	natural abundance		10 %

14 3D HN(COCA)CB

Instrument

Bruker Avance - 500 MHz four RF channels and triple-resonance cryoprobes with pulsed-field gradients

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 300 (±5) K, pH 7.3 (±0.2)

#	Name	Isotope labeling	Type	Concentration
1	MecA-NTD	[U-13C; U-15N]		1.0 mM
2	sodium chloride	natural abundance		140 mM
3	sodium phosphate	natural abundance		10 mM
4	potassium phosphate	natural abundance		1.8 mM
5	H2O	natural abundance		90 %
6	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_19755_2mk6.nef
Input source #2: Coordindates	2mk6.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
MEIERINEHTVKFYMSYGDIEDRGFDREEIWYNRERSEELFWEVMDEVHEEEEFAVEGPLWIQVQALDKGLEIIVTKAQLSKDLDKLVPR
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MEIERINEHTVKFYMSYGDIEDRGFDREEIWYNRERSEELFWEVMDEVHEEEEFAVEGPLWIQVQALDKGLEIIVTKAQLSKDLDKLVPR

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_19755_2mk6.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1027		100.0 (chain: A, length: 90)
1	Distance restraints	DYANA/DIANA_distance_constraints_2	Warning	3011 (1)	noe	98.9 (chain: A, length: 90)
1	Dihedral angle restraints	DYANA/DIANA_dihedral_3	OK	131 (131)	.	84.4 (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: 100.0%
- Total number of assignments
  - ¹H chemical shifts: 528
  - ¹³C chemical shifts: 409
  - ¹⁵N chemical shifts: 90
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: DYANA/DIANA_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 98.9%
- Total number of restraints: 3011
- Weight of restraints: 1.0 (3011)
- Potential type of restraints: upper-bound-parabolic (3011)
- Range of distance target values: 0.0, 6.67 (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: DYANA/DIANA_dihedral_3
- Status: OK
- Experiment type: .
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 90, Sequence coverage: 84.4%
- Total number of restraints: 131
- Total number of restraints per polymer type: 131
- Weight of restraints: 1.0 (131)
- Potential type of restraints: square-well-parabolic (131)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords competence, MecA, proteolysis