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- PDB-2rb2: 3-methylbenzylazide in complex with T4 lysozyme L99A -

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Basic information

Entry
Database: PDB / ID: 2rb2
Title3-methylbenzylazide 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 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
1-(azidomethyl)-3-methylbenzene / PHOSPHATE ION / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.463 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 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)18,7915
Polymers18,3591
Non-polymers4324
Water5,639313
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.240, 60.240, 96.837
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.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-263 / 1-(azidomethyl)-3-methylbenzene


Mass: 147.177 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H9N3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 55.47 %
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: 1.463→52.2 Å / Num. all: 35646 / Num. obs: 35646 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.023 / Net I/σ(I): 12.4
Reflection shellResolution: 1.463→1.52 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.348 / Num. unique all: 3485 / Χ2: 1.02 / % possible all: 99.1

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3data extraction
HKL-2000data collection
REFMACphasing
RefinementResolution: 1.463→52.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.127 / SU ML: 0.038 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.08 / ESU R Free: 0.071 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1789 5 %RANDOM
Rwork0.18 ---
all0.181 35586 --
obs0.181 35586 99.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.195 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20.19 Å20 Å2
2--0.39 Å20 Å2
3----0.58 Å2
Refinement stepCycle: LAST / Resolution: 1.463→52.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1315 0 26 320 1661
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221364
X-RAY DIFFRACTIONr_angle_refined_deg1.0831.9661848
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.535173
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23722.96964
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.60815249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3111515
X-RAY DIFFRACTIONr_chiral_restr0.0640.2204
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021022
X-RAY DIFFRACTIONr_nbd_refined0.3370.2713
X-RAY DIFFRACTIONr_nbtor_refined0.3180.2959
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2252
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1250.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1510.240
X-RAY DIFFRACTIONr_mcbond_it0.871.5844
X-RAY DIFFRACTIONr_mcangle_it1.07521321
X-RAY DIFFRACTIONr_scbond_it2.5263590
X-RAY DIFFRACTIONr_scangle_it2.7344.5521
X-RAY DIFFRACTIONr_rigid_bond_restr2.2831434
X-RAY DIFFRACTIONr_sphericity_free2.8033320
X-RAY DIFFRACTIONr_sphericity_bonded2.16131341
LS refinement shellResolution: 1.463→1.501 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 138 -
Rwork0.256 2337 -
all-2475 -
obs--94.86 %

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