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- PDB-4w56: T4 Lysozyme L99A with sec-Butylbenzene Bound -

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Basic information

Entry
Database: PDB / ID: 4w56
TitleT4 Lysozyme L99A with sec-Butylbenzene 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
(2R)-butan-2-ylbenzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 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

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0643
Polymers19,6921
Non-polymers3732
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint6 kcal/mol
Surface area8570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.360, 60.360, 96.820
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-3GY / (2R)-butan-2-ylbenzene / sec-Butylbenzene


Mass: 134.218 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14
#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.: 159 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
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: Jul 23, 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: 1.63→50 Å / Num. obs: 30214 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 15.34 Å2 / Rmerge F obs: 0.068 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.069 / Χ2: 1.012 / Net I/σ(I): 22.09 / Num. measured all: 226096
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
1.63-1.730.3020.4775.3436773417441740.506100
1.73-1.850.2050.3117.7834510388838880.33100
1.85-20.1190.18312.1432968371437140.194100
2-2.240.0660.120.7135811404240420.107100
2.24-2.680.0410.06629.5336187416641660.07100
2.68-3.280.0270.04837.222673271127100.051100
3.28-4.630.0170.03350.7617667213021260.03599.8
4.63-100.0160.0351.348745111111020.03399.2
100.0150.02744.387621441290.0389.6

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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: 1.63→45.997 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1877 1042 4 %Random selection
Rwork0.1709 25007 --
obs0.1716 26049 99.89 %-
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.887 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso max: 64 Å2 / Biso mean: 17.3165 Å2 / Biso min: 7.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.8345 Å2-0 Å2-0 Å2
2--0.8345 Å20 Å2
3----1.669 Å2
Refinement stepCycle: final / Resolution: 1.63→45.997 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 35 159 1478
Biso mean--26.55 27.26 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071448
X-RAY DIFFRACTIONf_angle_d0.9931964
X-RAY DIFFRACTIONf_chiral_restr0.059217
X-RAY DIFFRACTIONf_plane_restr0.005252
X-RAY DIFFRACTIONf_dihedral_angle_d10.975557
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.63-1.7160.20941450.18134953640100
1.716-1.82350.21391460.175935083654100
1.8235-1.96430.22211480.168235403688100
1.9643-2.16190.16091480.158335643712100
2.1619-2.47470.20221480.159735523700100
2.4747-3.11780.20091510.181736123763100
3.1178-46.01570.16861560.17193736389299

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