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BMRB: 19752

2MK5

Solution structure of a protein domain

Authors

Feng, Y., Gu, J.

Assembly

LysGH15

Entity

1. LysGH15 (polymer, Thiol state: all free), 131 monomers, 14034.62 Da Detail

SNAKNYMDKG TSSSTVVKDG KTSSASTPAT RPVTGSWKKN QYGTWYKPEN ATFVNGNQPI VTRIGSPFLN APVGGNLPAG ATIVYDEVCI QAGHIWIGYN AYNGNRVYCP VRTCQGVPPN HIPGVAWGVF K

Formula weight

14034.62 Da

Source organism

Staphylococcus phage G15

Exptl. method

Refine. method

molecular dynamics, simulated annealing

Data set

assigned_chemical_shifts

Chem. Shift Complete

Sequence coverage: 98.5 %, Completeness: 97.5 %, Completeness (bb): 97.4 % Detail

Polymer type: polypeptide(L)

	Total	¹H	¹³C	¹⁵N
All	97.5 % (1432 of 1469)	97.0 % (735 of 758)	98.2 % (561 of 571)	97.1 % (136 of 140)
Backbone	97.4 % (744 of 764)	96.6 % (257 of 266)	98.1 % (371 of 378)	96.7 % (116 of 120)
Sidechain	97.7 % (802 of 821)	97.2 % (478 of 492)	98.4 % (304 of 309)	100.0 % (20 of 20)
Aromatic	95.1 % (135 of 142)	94.4 % (67 of 71)	95.5 % (64 of 67)	100.0 % (4 of 4)
Methyl	100.0 % (130 of 130)	100.0 % (65 of 65)	100.0 % (65 of 65)

1. entity

SNAKNYMDKG TSSSTVVKDG KTSSASTPAT RPVTGSWKKN QYGTWYKPEN ATFVNGNQPI VTRIGSPFLN APVGGNLPAG ATIVYDEVCI QAGHIWIGYN AYNGNRVYCP VRTCQGVPPN HIPGVAWGVF K

Show sample condition

Sample

Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

LACS Plot; CA

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; CB

Referencing offset: -0.07 ppm, Outliers: 2 Detail

LACS Plot; HA

Referencing offset: -0.06 ppm, Outliers: 1 Detail

LACS Plot; CO

Referencing offset: 0.32 ppm, Outliers: 2 Detail

Protein Blocks Logo

Calculated from 20 models in PDB: 2MK5, Strand ID: A Detail

Release date

2014-05-26

Citation

Structural and biochemical characterization reveals LysGH15 as an unprecedented "EF-hand-like" calcium-binding phage lysin
Gu, J., Feng, Y., Feng, X., Sun, C., Lei, L., Ding, W., Niu, F., Jiao, L., Yang, M., Li, Y., Liu, X., Song, J., Cui, Z., Han, D., Du, C., Yang, Y., Ouyang, S., Liu, Z., Han, W.
PLoS Pathog. (2014), 10, e1004109-e1004109, PubMed 24831957 , DOI 10.1371/journal.ppat.1004109 , Abstract

Related entities 1. LysGH15, : 1 : 9 entities Detail

Experiments performed 12 experiments Detail

1 2D 1H-15N HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

2 2D 1H-13C HSQC

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

3 3D CBCA(CO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

4 3D HNCACB

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

5 3D HNCO

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

6 3D HN(CA)CO

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

7 3D HBHA(CO)NH

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

8 3D HCCH-TOCSY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

9 3D CCH-TOCSY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

10 3D 1H-15N NOESY

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

11 3D 1H-13C NOESY aliphatic

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

12 3D 1H-13C NOESY aromatic

Instrument

Agilent DD2 - 600 MHz

Sample

State isotropic, Solvent system 90% H2O/10% D2O, Pressure 1 atm, Temperature 298 K, pH 6.5

#	Name	Isotope labeling	Type	Concentration
1	entity	[U-13C; U-15N]		1.1 mM
2	sodium phosphate	natural abundance		40 mM
3	sodium chloride	natural abundance		50 mM
4	DSS	natural abundance		0.02 %
5	D2O	natural abundance		10 %
6	H2O	natural abundance		90 %

NMR combined restraints 5 contents Detail

Properties

Input source #1: NMR data (NEF) - Assigned chemical shifts, Distance restraints, Dihedral angle restraints	combined_19752_2mk5.nef
Input source #2: Coordindates	2mk5.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-------100
SNAKNYMDKGTSSSTVVKDGKTSSASTPATRPVTGSWKKNQYGTWYKPENATFVNGNQPIVTRIGSPFLNAPVGGNLPAGATIVYDEVCIQAGHIWIGYN
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
SNAKNYMDKGTSSSTVVKDGKTSSASTPATRPVTGSWKKNQYGTWYKPENATFVNGNQPIVTRIGSPFLNAPVGGNLPAGATIVYDEVCIQAGHIWIGYN

-------110-------120-------130-
AYNGNRVYCPVRTCQGVPPNHIPGVAWGVFK
|||||||||||||||||||||||||||||||
AYNGNRVYCPVRTCQGVPPNHIPGVAWGVFK

Chain assignments

Entity_assembly_ID (NMR)	Auth_asym_ID (model)	Length	Unmapped	Conflict	Sequence coverage (%)
A	A	131	0	0	100.0

Content subtype: combined_19752_2mk5.nef

#	Content subtype	Saveframe	Status	# of rows (sets)	Experiment type	Sequence coverage (%)
1	Assigned chemical shifts	assigned_chem_shift_list_1	Warning	1435		98.5 (chain: A, length: 131)
1	Distance restraints	CNS/XPLOR_distance_constraints_2	OK	6878 (1)	noe	97.7 (chain: A, length: 131)
2	Distance restraints	CNS/XPLOR_distance_constraints_3	OK	82 (1)	hbond	40.5 (chain: A, length: 131)
1	Dihedral angle restraints	CNS/XPLOR_dihedral_4	OK	168 (168)	.	73.3 (chain: A, length: 131)

Assigned chemical shifts

Saveframe: assigned_chem_shift_list_1
- Status: Warning
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 98.5%
- Total number of assignments
  - ¹H chemical shifts: 739
  - ¹³C chemical shifts: 560
  - ¹⁵N chemical shifts: 136
- Completeness of assignments
  - Entity_assemble_ID: A
- Redox state of CYS
- 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: CNS/XPLOR_distance_constraints_2
- Status: OK
- Experiment type: noe
- Sequence coverage of experimental data
  - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 97.7%
- Total number of restraints: 6875
- Weight of restraints: 1.0 (6875)
- Potential type of restraints: square-well-parabolic (6875)
- Range of distance target values: 2.3, 4.15 (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: OK
  - Experiment type: hbond
  - Sequence coverage of experimental data
    - Entity_assembly_ID: A, Chain length: 131, Sequence coverage: 40.5%
  - Total number of restraints: 82
  - Weight of restraints: 1.0 (82)
  - Potential type of restraints: square-well-parabolic (82)
  - Range of distance target values: 2.0, 3.0 (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: 131, Sequence coverage: 73.3%
- Total number of restraints: 168
- Total number of restraints per polymer type: 168
- Weight of restraints: 1.0 (168)
- Potential type of restraints: square-well-parabolic (168)
- Plot of Phi-Psi angle restraints
- Dihedral angle restraints per residue
  - Chain_ID: A

Keywords HYDROLASE