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- PDB-4w55: T4 Lysozyme L99A with n-Propylbenzene Bound -

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Basic information

Entry
Database: PDB / ID: 4w55
TitleT4 Lysozyme L99A with n-Propylbenzene 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
propylbenzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6401 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_assembly / pdbx_struct_assembly_prop / 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_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _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.d_res_high / _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)20,0503
Polymers19,6921
Non-polymers3582
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area450 Å2
ΔGint6 kcal/mol
Surface area8390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.320, 60.320, 96.490
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-3H0 / propylbenzene


Mass: 120.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H12
#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.: 157 / 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: 2.57 Å3/Da / Density % sol: 52.2 %
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 10, 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: 1.64→50 Å / Num. obs: 27463 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / Biso Wilson estimate: 15.83 Å2 / Rmerge F obs: 0.076 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.066 / Χ2: 0.973 / Net I/σ(I): 23.64 / Num. measured all: 226432
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
1.64-1.740.370.4884.5636530408140810.519100
1.74-1.850.2530.336.6231573351235120.351100
1.85-1.960.1580.21110.0625326281528150.224100
1.96-2.140.0890.12416.7430887342434240.132100
2.14-2.40.0580.07825.2329895332733270.082100
2.4-2.770.040.05932.8225467285928590.063100
2.77-3.380.0270.04144.7820899240624060.043100
3.38-4.770.0150.02761.5416492195119510.029100
4.770.0140.02561.389363114411430.02799.9

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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: 1.6401→45.938 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 16.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 1276 5 %Random selection
Rwork0.1664 24239 --
obs0.1674 25515 99.99 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.442 Å2 / ksol: 0.393 e/Å3
Displacement parametersBiso max: 63 Å2 / Biso mean: 17.5808 Å2 / Biso min: 7.82 Å2
Baniso -1Baniso -2Baniso -3
1-1.0739 Å2-0 Å2-0 Å2
2--1.0739 Å20 Å2
3----2.1478 Å2
Refinement stepCycle: final / Resolution: 1.6401→45.938 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 33 157 1472
Biso mean--26.35 28.09 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121433
X-RAY DIFFRACTIONf_angle_d1.2891943
X-RAY DIFFRACTIONf_chiral_restr0.079214
X-RAY DIFFRACTIONf_plane_restr0.006250
X-RAY DIFFRACTIONf_dihedral_angle_d12.893546
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.6401-1.70570.24741380.191326342772
1.7057-1.78340.1991410.174526682809
1.7834-1.87740.19831390.167526522791
1.8774-1.9950.20271400.15726552795
1.995-2.1490.18131410.153426762817
2.149-2.36530.18261410.159926722813
2.3653-2.70750.20221420.176427062848
2.7075-3.4110.20471430.170827172860
3.411-45.95640.15971510.162828593010

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