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- PDB-2rbs: (r)(+)-3-chloro-1-phenyl-1-propanol in complex with T4 lysozyme L... -

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Basic information

Entry
Database: PDB / ID: 2rbs
Title(r)(+)-3-chloro-1-phenyl-1-propanol in complex with T4 lysozyme L99A/M102Q
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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(1R)-3-chloro-1-phenylpropan-1-ol / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.557 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 19, 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: Refinement description / Category: software
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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7514
Polymers18,3901
Non-polymers3613
Water4,972276
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.368, 60.368, 96.895
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: 18390.061 Da / Num. of mol.: 1 / Mutation: L99A/M102Q
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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-269 / (1R)-3-chloro-1-phenylpropan-1-ol


Mass: 170.636 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11ClO
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 55.61 %
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: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115872 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 3, 2007 / Details: KOHZU: Double Crystal Si(111)
RadiationMonochromator: KHOZU Double flat crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115872 Å / Relative weight: 1
ReflectionResolution: 1.55→52.27 Å / Num. all: 29769 / Num. obs: 29769 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.3 % / Rmerge(I) obs: 0.106 / Χ2: 0.992 / Net I/σ(I): 11.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.55-1.615.90.36129230.959100
1.61-1.676.20.32129690.90399.9
1.67-1.756.40.25729110.97100
1.75-1.846.50.21829251.031100
1.84-1.956.50.18929501.036100
1.95-2.16.40.13129470.95100
2.1-2.326.20.1229841.0899.9
2.32-2.656.30.09729800.988100
2.65-3.346.20.08330300.998100
3.34-506.50.08831500.99799.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
REFMACphasing
RefinementStarting model: 1LGU

1lgu


Resolution: 1.557→52.27 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.951 / SU B: 2.674 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.101 / ESU R Free: 0.078 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1504 5.1 %RANDOM
Rwork0.183 ---
all0.184 29676 --
obs0.184 29676 99.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0.16 Å20 Å2
2---0.32 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 1.557→52.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 32 285 1634
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221373
X-RAY DIFFRACTIONr_angle_refined_deg1.1271.971855
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8975172
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64423.69265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.08615253
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.4121513
X-RAY DIFFRACTIONr_chiral_restr0.0780.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021026
X-RAY DIFFRACTIONr_nbd_refined0.1890.2686
X-RAY DIFFRACTIONr_nbtor_refined0.3040.2946
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2209
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1760.230
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.221
X-RAY DIFFRACTIONr_mcbond_it0.7661.5849
X-RAY DIFFRACTIONr_mcangle_it1.1721319
X-RAY DIFFRACTIONr_scbond_it1.9183603
X-RAY DIFFRACTIONr_scangle_it2.6124.5530
X-RAY DIFFRACTIONr_rigid_bond_restr1.1131452
X-RAY DIFFRACTIONr_sphericity_free3.1443285
X-RAY DIFFRACTIONr_sphericity_bonded1.94731349
LS refinement shellResolution: 1.557→1.598 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 100 -
Rwork0.196 1930 -
all-2030 -
obs--93.59 %

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