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- PDB-2oe7: High-Pressure T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2oe7
TitleHigh-Pressure T4 Lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / High-pressure / T4 Lysozyme
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
BETA-MERCAPTOETHANOL / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / ISOMORPHOUS REPLACEMENT / Resolution: 2.1 Å
AuthorsCollins, M.D. / Quillin, M.L. / Matthews, B.W. / Gruner, S.M.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Structural Rigidity of a Large Cavity-containing Protein Revealed by High-pressure Crystallography.
Authors: Collins, M.D. / Quillin, M.L. / Hummer, G. / Matthews, B.W. / Gruner, S.M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Cooperative water filling of a nonpolar protein cavity observed by high-pressure crystallography and simulation.
Authors: Collins, M.D. / Quillin, M.L. / Hummer, G. / Matthews, B.M. / Gruner, S.M.
History
DepositionDec 28, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 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 1.5Aug 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)18,8565
Polymers18,6281
Non-polymers2274
Water3,261181
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.715, 60.715, 96.009
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 / Lysis protein / Muramidase / Endolysin


Mass: 18628.363 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 / Genus (production host): T4-like viruses
Species (production host): Enterobacteria phage T4 sensu lato
Production host: Enterobacteria phage T4 (virus) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: ~2.0 M NA/K PHOSPHATES, 50 MM BETA-MERCAPTOETHANOL, PH 7.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9174
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 15, 2004
RadiationMonochromator: Si xtal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9174 Å / Relative weight: 1
ReflectionResolution: 2.1→60 Å / Num. obs: 11985 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Redundancy: 7.5 % / Rmerge(I) obs: 0.041 / Χ2: 1.264 / Net I/σ(I): 22.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.185.80.11511421.33992.5
2.18-2.267.70.112241.436100
2.26-2.375.20.0839151.43174.9
2.37-2.497.80.06312081.20898.5
2.49-2.658.40.05412721.164100
2.65-2.858.40.04412421.153100
2.85-3.148.30.03912451.223100
3.14-3.598.20.03312601.26699.6
3.59-4.527.60.03112331.27896.8
4.52-6070.02912441.28990.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0005refinement
PDB_EXTRACT2data extraction
ADSCQUANTUMdata collection
RefinementMethod to determine structure: ISOMORPHOUS REPLACEMENT
Starting model: pdb entry 1L63

1l63


Resolution: 2.1→52.56 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 3.627 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.214 598 5 %RANDOM
Rwork0.157 ---
obs0.16 11939 95.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.695 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 2.1→52.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 181 1483
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0221318
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9551771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9915161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84323.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2971513
X-RAY DIFFRACTIONr_chiral_restr0.090.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02976
X-RAY DIFFRACTIONr_nbd_refined0.1960.2614
X-RAY DIFFRACTIONr_nbtor_refined0.3020.2920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2145
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1750.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.228
X-RAY DIFFRACTIONr_mcbond_it1.1611.5834
X-RAY DIFFRACTIONr_mcangle_it1.73321284
X-RAY DIFFRACTIONr_scbond_it3.2923560
X-RAY DIFFRACTIONr_scangle_it5.2844.5487
LS refinement shellResolution: 2.1→2.15 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 53 -
Rwork0.17 797 -
obs-850 94.34 %

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