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- PDB-4ekr: T4 Lysozyme L99A/M102H with 2-Cyanophenol Bound -

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Basic information

Entry
Database: PDB / ID: 4ekr
TitleT4 Lysozyme L99A/M102H with 2-Cyanophenol Bound
ComponentsLysozyme
KeywordsHYDROLASE / Alkylation of Cys97
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-hydroxybenzonitrile / ACETATE ION / BETA-MERCAPTOETHANOL / 2-HYDROXYETHYL DISULFIDE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsMerski, M. / Shoichet, B.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Engineering a model protein cavity to catalyze the Kemp elimination.
Authors: Merski, M. / Shoichet, B.K.
History
DepositionApr 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2012Group: Database references
Revision 1.2Oct 17, 2012Group: Database references
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17517
Polymers42,8092
Non-polymers1,36615
Water5,549308
1
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,2049
Polymers21,4041
Non-polymers8008
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,9718
Polymers21,4041
Non-polymers5677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Lysozyme
hetero molecules

B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,17517
Polymers42,8092
Non-polymers1,36615
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-x+1,y-1/2,-z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area16230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.170, 75.630, 52.800
Angle α, β, γ (deg.)90.000, 93.210, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysozyme / Endolysin / Lysis protein / Muramidase


Mass: 21404.426 Da / Num. of mol.: 2 / Mutation: T21C/S38D/L99A/M102H/E108V/S117V/T142C/N144D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: E / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme

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Non-polymers , 6 types, 323 molecules

#2: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-0R0 / 2-hydroxybenzonitrile / 2-Cyanophenol


Mass: 119.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H5NO
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-HED / 2-HYDROXYETHYL DISULFIDE


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 308 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 30% (w/v) PEG-6000, 0.3 M LiSO4, 3% (w/v) TMAO, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.116 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 22, 2010
RadiationMonochromator: two flat Si(111) crystals, mounted in a model DCM from Khozu
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.116 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 57470 / % possible obs: 93.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.046 / Net I/σ(I): 15.12
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsDiffraction-ID% possible all
1.49-1.570.3323.06220368557195.8
1.57-1.670.2274.38222198542195.9
1.67-1.780.1526.44190457256195.5
1.78-1.920.1079.2184256945194.8
1.92-2.110.06714.13178906677193.7
2.11-2.360.04621.11154045707192.4
2.36-2.720.03427.46133964901190.7
2.72-3.330.02832.39114404120188.7
3.33-4.710.0243.4789143117186.4
4.71-500.01846.4249541648182

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction