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- PDB-2ray: beta-chlorophenetole in complex with T4 lysozyme L99A -

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Basic information

Entry
Database: PDB / ID: 2ray
Titlebeta-chlorophenetole in complex with T4 lysozyme L99A
ComponentsLysozyme
KeywordsHYDROLASE / protein cavities
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-chloroethoxy)benzene / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.798 Å
AuthorsGraves, A.P. / Boyce, S.E. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Rescoring docking hit lists for model cavity sites: predictions and experimental testing.
Authors: Graves, A.P. / Shivakumar, D.M. / Boyce, S.E. / Jacobson, M.P. / Case, D.A. / Shoichet, B.K.
History
DepositionSep 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 20, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6113
Polymers18,3591
Non-polymers2522
Water3,819212
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.462, 60.462, 96.004
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 Lysozyme / / E.C.3.2.1.17 / Lysis protein / Muramidase / Endolysin


Mass: 18359.023 Da / Num. of mol.: 1 / Mutation: L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: E / Plasmid: M13 / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-258 / (2-chloroethoxy)benzene


Mass: 156.609 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9ClO
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 212 / 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: 2.76 Å3/Da / Density % sol: 55.41 %
Crystal growTemperature: 277 K / Method: hanging drop / pH: 7.1
Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, hanging drop, temperature 277K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 26, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.798→52.34 Å / Num. all: 19492 / Num. obs: 19434 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.798→1.84 Å / % possible all: 98.9

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
HKL-3000data scaling
REFMAC5.2phasing
RefinementStarting model: 184L
Resolution: 1.798→52.34 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.374 / SU ML: 0.075 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 994 5.1 %RANDOM
Rwork0.187 ---
all0.188 19464 --
obs0.188 19408 99.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.548 Å2
Baniso -1Baniso -2Baniso -3
1-0.12 Å20.06 Å20 Å2
2--0.12 Å20 Å2
3----0.19 Å2
Refinement stepCycle: LAST / Resolution: 1.798→52.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1285 0 15 213 1513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221309
X-RAY DIFFRACTIONr_angle_refined_deg1.2491.9591766
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.255163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.47823.83360
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.22315233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.871511
X-RAY DIFFRACTIONr_chiral_restr0.0880.2196
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02977
X-RAY DIFFRACTIONr_nbd_refined0.1970.2649
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2908
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2163
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1830.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.230
X-RAY DIFFRACTIONr_mcbond_it0.7861.5830
X-RAY DIFFRACTIONr_mcangle_it1.23621285
X-RAY DIFFRACTIONr_scbond_it2.1733555
X-RAY DIFFRACTIONr_scangle_it3.194.5480
LS refinement shellResolution: 1.798→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.302 75 -
Rwork0.278 1314 -
all-1389 -
obs-1904 98.93 %

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