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- PDB-2oea: High-pressure structure of pseudo-WT T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2oea
TitleHigh-pressure structure of pseudo-WT 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: 2.01 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
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.548, 60.548, 95.525
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 / Plasmid: M13 2 / 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.: 231 / 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: 2.71 Å3/Da / Density % sol: 54.66 %
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→60 Å / Num. obs: 12994 / % possible obs: 90.5 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.057 / Χ2: 1.897 / Net I/σ(I): 20.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2-2.072.30.1584861.7634.6
2.07-2.154.30.11913781.51196.8
2.15-2.254.90.10513791.69798.3
2.25-2.3740.08911671.70383.1
2.37-2.525.70.07514161.68599.4
2.52-2.715.80.06714011.74799.9
2.71-2.995.80.05814331.93699.9
2.99-3.425.70.05314432.18799.9
3.42-4.315.50.04714292.33998.4
4.31-6050.04214622.06193.7

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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: 2.01→52.41 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.174 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.166 / ESU R Free: 0.158 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.213 658 5.1 %RANDOM
Rwork0.159 ---
obs0.161 12956 92.68 %-
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: 22.405 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.01→52.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 231 1533
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221318
X-RAY DIFFRACTIONr_angle_refined_deg1.281.9551771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.02523.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.42915245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.8021513
X-RAY DIFFRACTIONr_chiral_restr0.0850.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02976
X-RAY DIFFRACTIONr_nbd_refined0.2030.2637
X-RAY DIFFRACTIONr_nbtor_refined0.3030.2925
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1960.230
X-RAY DIFFRACTIONr_mcbond_it1.0961.5833
X-RAY DIFFRACTIONr_mcangle_it1.60821284
X-RAY DIFFRACTIONr_scbond_it3.0923562
X-RAY DIFFRACTIONr_scangle_it4.9794.5487
LS refinement shellResolution: 2.01→2.063 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 24 -
Rwork0.208 397 -
obs-421 42.23 %

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