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- PDB-4w58: T4 Lysozyme L99A with n-Pentylbenzene Bound -

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Basic information

Entry
Database: PDB / ID: 4w58
TitleT4 Lysozyme L99A with n-Pentylbenzene 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
pentylbenzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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.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)20,0783
Polymers19,6921
Non-polymers3872
Water2,324129
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area470 Å2
ΔGint6 kcal/mol
Surface area8560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.690, 60.690, 97.140
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-3H2 / pentylbenzene


Mass: 148.245 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16
#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.: 129 / 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: 2.62 Å3/Da / Density % sol: 53.1 %
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: Jun 30, 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: 1.8→50 Å / Num. obs: 23258 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Biso Wilson estimate: 16.46 Å2 / Rmerge F obs: 0.074 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.089 / Χ2: 1.036 / Net I/σ(I): 20.5 / Num. measured all: 176887
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
1.8-1.910.2780.4815.8629122318631860.51100
1.91-2.050.1740.3019.2428365309830980.319100
2.05-2.280.0990.1614.9233016361036100.17100
2.28-2.550.0680.10920.1225140276527640.116100
2.55-2.940.0510.08225.1221590241624160.087100
2.94-3.60.0330.05334.2517988209320930.057100
3.6-5.080.020.03745.1413850164216420.04100
5.080.0190.03443.4678169759730.03799.8

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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: 1.8→46.226 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 15.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1843 1186 6 %Random selection
Rwork0.1611 18593 --
obs0.1624 19779 99.97 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 61.984 Å2 / ksol: 0.438 e/Å3
Displacement parametersBiso max: 73.15 Å2 / Biso mean: 18.4039 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.7269 Å2-0 Å2-0 Å2
2--1.7269 Å20 Å2
3----3.4537 Å2
Refinement stepCycle: final / Resolution: 1.8→46.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 26 129 1447
Biso mean--27.04 30.01 -
Num. residues----165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161489
X-RAY DIFFRACTIONf_angle_d1.4892026
X-RAY DIFFRACTIONf_chiral_restr0.103224
X-RAY DIFFRACTIONf_plane_restr0.007260
X-RAY DIFFRACTIONf_dihedral_angle_d11.759588
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.88190.25361460.178822862432
1.8819-1.98110.1981450.153122832428
1.9811-2.10530.16641480.13723182466
2.1053-2.26780.14721450.135522632408
2.2678-2.4960.21551470.14923152462
2.496-2.85720.2071480.170423162464
2.8572-3.59950.17681510.156223542505
3.5995-46.24160.17031560.178524582614

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