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- PDB-4w59: T4 Lysozyme L99A with n-Hexylbenzene Bound -

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Basic information

Entry
Database: PDB / ID: 4w59
TitleT4 Lysozyme L99A with n-Hexylbenzene Bound
ComponentsEndolysin
KeywordsHYDROLASE
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
hexylbenzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.39 Å
AuthorsMerski, M. / Shoichet, B.K. / Eidam, O. / Fischer, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM59957 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Homologous ligands accommodated by discrete conformations of a buried cavity.
Authors: Merski, M. / Fischer, M. / Balius, T.E. / Eidam, O. / Shoichet, B.K.
History
DepositionAug 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 22, 2015Group: Database references
Revision 1.2May 6, 2015Group: Database references
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0923
Polymers19,6921
Non-polymers4012
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.410, 60.410, 96.560
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 19691.541 Da / Num. of mol.: 1 / Mutation: L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Plasmid: pET29 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-3GZ / hexylbenzene


Mass: 162.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.58 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% (w/v) PEGF-4000, 10% 2-propanol, 0.1 M HEPES, 50 mM 2-mercaptoethanol, 50 mM 2-hydroxyethyl disulfide

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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: May 29, 2009
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: 1.39→50 Å / Num. obs: 45280 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 13.45 Å2 / Rmerge F obs: 0.075 / Rmerge(I) obs: 0.049 / Rrim(I) all: 0.053 / Χ2: 1.005 / Net I/σ(I): 21.22 / Num. measured all: 293546
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.39-1.480.4720.5293.748537705070490.573100
1.48-1.580.2450.2856.7642945607960780.308100
1.58-1.690.160.18510.0436696511951190.199100
1.69-1.810.1080.12614.2330860427742760.136100
1.81-2.020.060.07721.9838234529652960.083100
2.02-2.340.0340.04734.1334591484648460.051100
2.34-2.860.0250.0441.627971400340010.043100
2.86-4.040.0160.02850.6921965319131870.0399.9
4.04-100.0130.02453.311270170216850.02699
100.0170.02542.554771421090.02976.8

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.15data extraction
PHENIX(phenix.refine: 1.7.1_743)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 181L

181l


Resolution: 1.39→45.999 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 1250 3 %Random selection
Rwork0.1757 40395 --
obs0.176 41645 99.86 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.888 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso max: 46.97 Å2 / Biso mean: 16.1706 Å2 / Biso min: 6.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.9387 Å20 Å20 Å2
2--0.9387 Å20 Å2
3----1.8774 Å2
Refinement stepCycle: final / Resolution: 1.39→45.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 27 185 1507
Biso mean--22.25 26.43 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121460
X-RAY DIFFRACTIONf_angle_d1.2541983
X-RAY DIFFRACTIONf_chiral_restr0.068219
X-RAY DIFFRACTIONf_plane_restr0.006255
X-RAY DIFFRACTIONf_dihedral_angle_d14.486568
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.39-1.44570.21741370.208944284565100
1.4457-1.51150.23241370.184444284565100
1.5115-1.59110.19341380.171644454583100
1.5911-1.69080.17371370.164944364573100
1.6908-1.82140.16771380.164544624600100
1.8214-2.00470.19041390.172944864625100
2.0047-2.29480.19321380.171644834621100
2.2948-2.89110.22541410.183745464687100
2.8911-46.02410.16091450.1744681482699

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