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- PDB-2oe4: High Pressure Psuedo Wild Type T4 Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2oe4
TitleHigh Pressure Psuedo Wild Type T4 Lysozyme
ComponentsLysozyme
KeywordsHYDROLASE / High-Pressure / T4 Lyzoyme
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.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Cooperative water filling of a non-polar protein cavity observed by high-pressure crystallography and simulation
Authors: Collins, M.D. / Hummer, G. / Quillin, M.L. / Matthews, B.W. / 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
Water3,099172
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.741, 60.741, 96.028
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.: 172 / 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: 55.19 %
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
RadiationProtocol: 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. all: 12341 / Num. obs: 12182 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.07 / Χ2: 2.052 / Net I/σ(I): 17.9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.202 / Num. unique all: 1156 / Χ2: 1.466 / % possible all: 93.7

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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: 2.1→52.63 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 4.012 / SU ML: 0.107 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.179 / ESU R Free: 0.172 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.222 609 5 %RANDOM
Rwork0.161 ---
obs0.164 12085 97.16 %-
all-12466 --
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: 24.649 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å2-0.06 Å20 Å2
2---0.12 Å20 Å2
3---0.18 Å2
Refine analyzeLuzzati coordinate error obs: 0.1 Å
Refinement stepCycle: LAST / Resolution: 2.1→52.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1292 0 10 172 1474
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221318
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.9551771
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1285161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.05523.38762
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76315245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9791513
X-RAY DIFFRACTIONr_chiral_restr0.0970.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02976
X-RAY DIFFRACTIONr_nbd_refined0.2040.2606
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2133
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.242
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2490.218
X-RAY DIFFRACTIONr_mcbond_it1.2071.5834
X-RAY DIFFRACTIONr_mcangle_it1.78421284
X-RAY DIFFRACTIONr_scbond_it3.4853567
X-RAY DIFFRACTIONr_scangle_it5.5624.5487
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 60 -
Rwork0.189 825 -
obs-885 99.22 %

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