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- PDB-4s0w: Wild type T4 lysozyme structure -

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Basic information

Entry
Database: PDB / ID: 4s0w
TitleWild type T4 lysozyme structure
ComponentsLysozyme
KeywordsHYDROLASE
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
Endolysin / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.117 Å
AuthorsSnell, E.H. / Snell, M.E.
CitationJournal: To be Published
Title: Wild type T4 lysozyme structure
Authors: Snell, E.H. / Snell, M.E.
History
DepositionJan 7, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 28, 2016Group: Database references / Structure summary
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,56814
Polymers37,3252
Non-polymers1,24412
Water6,071337
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3528
Polymers18,6621
Non-polymers6897
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2166
Polymers18,6621
Non-polymers5545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.630, 52.630, 99.460
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Lysozyme


Mass: 18662.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126 / Plasmid: pHS1403 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D9IEF7, UniProt: P00720*PLUS, lysozyme

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Non-polymers , 5 types, 349 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 337 / 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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 296 K / Method: batch under oil / pH: 7.5
Details: 0.5 M ammonium sulfate, 0.1 M HEPES, 30% MPD, pH 7.5, BATCH UNDER OIL, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 22, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 2.117→45.579 Å / Num. all: 17563 / Num. obs: 17563 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 5.9 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 8.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1683)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 206L

206l


Resolution: 2.117→33.601 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 2.04 / Phase error: 19.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 796 4.54 %RANDOM
Rwork0.1697 ---
obs0.1718 17534 99.98 %-
all-17563 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.117→33.601 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2584 0 71 337 2992
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032802
X-RAY DIFFRACTIONf_angle_d0.5593779
X-RAY DIFFRACTIONf_dihedral_angle_d10.0961088
X-RAY DIFFRACTIONf_chiral_restr0.024403
X-RAY DIFFRACTIONf_plane_restr0.001482
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.117-2.24980.26671180.17862804X-RAY DIFFRACTION100
2.2498-2.42350.23641370.17792771X-RAY DIFFRACTION100
2.4235-2.66730.24331320.18612801X-RAY DIFFRACTION100
2.6673-3.0530.22441320.1792788X-RAY DIFFRACTION100
3.053-3.84560.2051160.15412811X-RAY DIFFRACTION100
3.8456-33.60520.18591610.16122763X-RAY DIFFRACTION100

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