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- PDB-2oty: 1,2-dichlorobenzene in complex with T4 Lysozyme L99A -

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Basic information

Entry
Database: PDB / ID: 2oty
Title1,2-dichlorobenzene in complex with T4 Lysozyme L99A
ComponentsLysozyme
KeywordsHYDROLASE / PROTEIN-LIGAND COMPLEX / MODEL SYSTEM
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
BETA-MERCAPTOETHANOL / PHOSPHATE ION / 1,2-DICHLOROBENZENE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsGraves, A.P. / Shoichet, B.K.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Predicting absolute ligand binding free energies to a simple model site.
Authors: Mobley, D.L. / Graves, A.P. / Chodera, J.D. / McReynolds, A.C. / Shoichet, B.K. / Dill, K.A.
History
DepositionFeb 9, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / 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)18,8696
Polymers18,3591
Non-polymers5105
Water4,197233
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.210, 60.210, 97.031
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 18359.023 Da / Num. of mol.: 1
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-YAN / 1,2-DICHLOROBENZENE / 1,2-Dichlorobenzene


Mass: 147.002 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4Cl2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 2.2M sodium-potassium phosphate, 0.05M beta-mercaptoethanol, 0.05M 2-hydroxyethyldisulfide, pH 7.1, VAPOR DIFFUSION, 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: Jun 27, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. all: 22986 / Num. obs: 22986 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.8 % / Rmerge(I) obs: 0.098 / Χ2: 1.006 / Net I/σ(I): 9.8
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.645 / Num. unique all: 2263 / Χ2: 0.972 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data collection
HKL-2000data reduction
REFMAC5.2.0019phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 181L
Resolution: 1.83→52.13 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.875 / SU ML: 0.089 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.136 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.235 959 5.2 %RANDOM
Rwork0.196 ---
all0.206 22951 --
obs0.198 18469 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.79 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.83→52.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 35 237 1567
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221350
X-RAY DIFFRACTIONr_angle_refined_deg1.0041.9741822
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8225167
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.26323.27961
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.11215243
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5641513
X-RAY DIFFRACTIONr_chiral_restr0.0650.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021000
X-RAY DIFFRACTIONr_nbd_refined0.1820.2708
X-RAY DIFFRACTIONr_nbtor_refined0.2970.2933
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1140.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.10.223
X-RAY DIFFRACTIONr_mcbond_it0.4361.5846
X-RAY DIFFRACTIONr_mcangle_it0.67221302
X-RAY DIFFRACTIONr_scbond_it1.2853596
X-RAY DIFFRACTIONr_scangle_it1.8314.5516
LS refinement shellResolution: 1.83→1.877 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 58 -
Rwork0.27 1259 -
obs-1317 100 %

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