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BMRB: 25002

2MPW

Solution structure of the LysM region of the E. coli Intimin periplasmic domain

Authors

Coles, M., Chaubey, M., Leo, J.C., Linke, D., Schuetz, M.C., Goetz, F., Autenrieth, I.B.

Assembly

LysM region of the E. coli Intimin periplasmic domain

Entity

1. LysM region of the E. coli Intimin periplasmic domain (polymer, Thiol state: not present), 115 monomers, 12556.06 Da Detail

MNGENYFKLG SDSKLLTHNS YQNRLFYTLK TGETVADLSK SQDINLSTIW SLNKHLYSSE SEMMKAAPGQ QIILPLKKLP FEYSALPLLG SAPLVAAGGV AGHTNGSGSE NLYFQ

Formula weight

12556.06 Da

Source organism

Escherichia coli

Exptl. method

Refine. method

simulated annealing, NOESY back-calculation

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 79.1 %, Completeness: 67.9 %, Completeness (bb): 72.5 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	67.9 % (904 of 1331)	69.8 % (481 of 689)	64.7 % (335 of 518)	71.0 % (88 of 124)
Backbone	72.5 % (493 of 680)	74.0 % (174 of 235)	70.1 % (235 of 335)	76.4 % (84 of 110)
Sidechain	65.1 % (492 of 756)	67.6 % (307 of 454)	62.8 % (181 of 288)	28.6 % (4 of 14)
Aromatic	28.6 % (32 of 112)	46.4 % (26 of 56)	9.1 % (5 of 55)	100.0 % (1 of 1)
Methyl	81.5 % (101 of 124)	83.9 % (52 of 62)	79.0 % (49 of 62)

1. LysM

MNGENYFKLG SDSKLLTHNS YQNRLFYTLK TGETVADLSK SQDINLSTIW SLNKHLYSSE SEMMKAAPGQ QIILPLKKLP FEYSALPLLG SAPLVAAGGV AGHTNGSGSE NLYFQ

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

LACS Plot; CA

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: 0.12 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: 0.1 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.09 ppm, Outliers: 4 Detail

Protein Blocks Logo

Calculated from 23 models in PDB: 2MPW, Strand ID: A Detail

Release date

2014-11-09

Citation

The Intimin periplasmic domain mediates dimerisation and binding to peptidoglycan
Leo, J.C., Oberhettinger, P., Chaubey, M., Schuetz, M., Kuehner, D., Goetz, F., Coles, M., Autenrieth, I.B., Linke, D.
Mol. Microbiol. (2015), 95, 80-100, PubMed 25353290 , DOI 10.1111/mmi.12840 , Abstract

Related entities 1. LysM region of the E. coli Intimin periplasmic domain, : 1 : 1 : 6 entities Detail

Experiments performed 12 experiments Detail

1 3D HNCO

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

2 3D HNCA

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

3 3D C(CO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

4 3D HNCANNH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

5 3D HCCH-TOCSY

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

6 3D H(CCO)NH

Instrument

Bruker Avance - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

7 3D 1H-15N NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

8 3D 1H-13C NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

9 3D CNH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

10 3D NNH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

11 3D CCH-NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
6	LysM	[U-100% 13C; U-100% 15N]		0.5 mM
7	sodium phosphate	natural abundance		20 mM
8	sodium chloride	natural abundance		150 mM
9	H2O	natural abundance		90 %
10	D2O	natural abundance		10 %

12 2D 12C-filtered 1H-1H NOESY

Instrument

Bruker Avance - 800 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 7.4

#	Name	Isotope labeling	Type	Concentration
1	LysM	[U-100% 15N]		0.5 mM
2	sodium phosphate	natural abundance		20 mM
3	sodium chloride	natural abundance		150 mM
4	H2O	natural abundance		90 %
5	D2O	natural abundance		10 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_25002_2mpw.nef
Input source #2: Coordindates	2mpw.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

-40-------50--------60--------70--------80--------90-------100-------110-------120-------130-------1
MNGENYFKLGSDSKLLTHNSYQNRLFYTLKTGETVADLSKSQDINLSTIWSLNKHLYSSESEMMKAAPGQQIILPLKKLPFEYSALPLLGSAPLVAAGGV
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
MNGENYFKLGSDSKLLTHNSYQNRLFYTLKTGETVADLSKSQDINLSTIWSLNKHLYSSESEMMKAAPGQQIILPLKKLPFEYSALPLLGSAPLVAAGGV
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100

40-------150---
AGHTNGSGSENLYFQ
|||||||||||||||
AGHTNGSGSENLYFQ
-------110-----

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	115	0	0	100.0

Content subtype: combined_25002_2mpw.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	853		73.9 (chain: A, length: 115)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	Warning	207 (1)	noe	46.1 (chain: A, length: 115)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	30 (1)	hbond	36.5 (chain: A, length: 115)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	416 (416)	.	100.0 (chain: A, length: 115)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 73.9%
- Total number of assignments
  - ¹H chemical shifts: 456
  - ¹³C chemical shifts: 315
  - ¹⁵N chemical shifts: 82
- Completeness of assignments
  - Entity_assemble_ID: A
- 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

Distance restraints

Saveframe: CNS/XPLOR_distance_constraints_2
- Status: Warning
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 46.1%
- Total number of restraints: 207
- Weight of restraints: 1.0 (207)
- Potential type of restraints: square-well-parabolic (207)
- Range of distance target values: 1.35, 6.0 (Å)
- Histogram of distance target values
- Distance restraints per residue
  - Chain_ID: A
- Distance restraints on contact map
- Saveframe: CNS/XPLOR_distance_constraints_3
  - Status: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 115, Sequence coverage: 36.5%
  - Total number of restraints: 30
  - Weight of restraints: 1.0 (30)
  - Potential type of restraints: square-well-parabolic (30)
  - Range of distance target values: 2.2, 2.2 (Å)
  - 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: 115, Sequence coverage: 100.0%
- Total number of restraints: 416
- Total number of restraints per polymer type: 416
- Weight of restraints: 1.0 (416)
- Potential type of restraints: square-well-parabolic (416)
- Plot of Phi-Psi angle restraints
- Plot of Chi1-Chi2 angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords LysM, peptidoglycan-binding