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- PDB-2rb0: 2,6-difluorobenzylbromide complex with T4 lysozyme L99A -

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Basic information

Entry
Database: PDB / ID: 2rb0
Title2,6-difluorobenzylbromide 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-(bromomethyl)-1,3-difluorobenzene / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.84 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: 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

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Assembly

Deposited unit
X: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7564
Polymers18,3591
Non-polymers3973
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.287, 60.287, 96.861
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 / 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


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-260 / 2-(bromomethyl)-1,3-difluorobenzene


Mass: 207.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H5BrF2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / 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: 55.55 %
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: Nov 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.84→52.2 Å / Num. all: 14638 / Num. obs: 14638 / % possible obs: 80 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rmerge(I) obs: 0.077 / Χ2: 1.002 / Net I/σ(I): 16.3
Reflection shellResolution: 1.84→1.91 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.389 / Num. unique all: 1218 / Χ2: 1.04 / % possible all: 67.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
REFMACphasing
RefinementStarting model: 184L

184l


Resolution: 1.84→52.2 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.928 / SU B: 2.643 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.155 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.233 740 5.1 %RANDOM
Rwork0.196 ---
all0.198 14615 --
obs0.198 14615 80.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.992 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.84→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1287 0 20 194 1501
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221326
X-RAY DIFFRACTIONr_angle_refined_deg0.9861.9631790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.6525163
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.44523.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.98115239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0641513
X-RAY DIFFRACTIONr_chiral_restr0.0610.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02989
X-RAY DIFFRACTIONr_nbd_refined0.1790.2648
X-RAY DIFFRACTIONr_nbtor_refined0.2940.2913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2148
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1570.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.221
X-RAY DIFFRACTIONr_mcbond_it0.7061.5835
X-RAY DIFFRACTIONr_mcangle_it0.67321289
X-RAY DIFFRACTIONr_scbond_it1.5313574
X-RAY DIFFRACTIONr_scangle_it2.094.5500
LS refinement shellResolution: 1.84→1.887 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 32 -
Rwork0.323 772 -
all-804 -
obs--60.59 %

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