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- PDB-1p7s: T4 LYSOZYME CORE REPACKING MUTANT V103I/TA -

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Basic information

Entry
Database: PDB / ID: 1p7s
TitleT4 LYSOZYME CORE REPACKING MUTANT V103I/TA
ComponentsLYSOZYME
KeywordsHYDROLASE / HYDROLASE (O-GLYCOSYL) / T4 LYSOZYME / DESIGNED CORE MUTANT / AUTOMATED PROTEIN DESIGN / PROTEIN ENGINEERING / PROTEIN FOLDING / PROTEIN STABILITY / CORE REPACKING / BACK REVERTANT / DEAD-END ELIMINATION THEOREM / SIDE-CHAIN PACKING / OPTIMIZED ROTAMER COMBINATIONS / ORBIT
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
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Repacking the Core of T4 Lysozyme by Automated Design
Authors: Mooers, B.H. / Datta, D. / Baase, W.A. / Zollars, E.S. / Mayo, S.L. / Matthews, B.W.
History
DepositionMay 5, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 16, 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
A: LYSOZYME


Theoretical massNumber of molelcules
Total (without water)18,6421
Polymers18,6421
Non-polymers00
Water3,189177
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.787, 54.862, 88.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein LYSOZYME / Lysis protein / Muramidase / Endolysin


Mass: 18642.389 Da / Num. of mol.: 1 / Mutation: C54T/C97A/V103I
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 / Plasmid: PHS1403 / Production host: Escherichia coli (E. coli) / Strain (production host): RR1 / References: UniProt: P00720, lysozyme
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / 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 Å3/Da / Density % sol: 38.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 2M K/Na phosphate, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.1 MHEPES1reservoirpH7.5
220 %(w/v)PEG34001reservoir
35 %(v/v)isopropanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 1.23979 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 16, 2002
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23979 Å / Relative weight: 1
ReflectionResolution: 1.5→22.086 Å / Num. all: 23577 / Num. obs: 23577 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 17.163 Å2 / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/σ(I): 7.4
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.2 / Num. unique all: 2748 / Rsym value: 0.351 / % possible all: 77.9
Reflection
*PLUS
Highest resolution: 1.5 Å
Reflection shell
*PLUS
% possible obs: 78 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1L63

1l63


Resolution: 1.5→22.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT
Details: THE WORKING SET AND TEST SET WERE NOT COMBINED DURING THE LAST STAGE OF REFINEMENT. THE OVERALL ANISOTROPIC B-VALUES ARE B11=0.34, B22=-0.02, B12=B13=B23=0.0, B33=-1.32
RfactorNum. reflection% reflectionSelection details
Rfree0.266 625 3 %RANDOM
Rwork0.192 ---
obs0.193 23532 95 %-
all-23532 --
Solvent computationSolvent model: TNT / Bsol: 248.48 Å2 / ksol: 0.85 e/Å3
Refinement stepCycle: LAST / Resolution: 1.5→22.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1321 0 0 177 1498
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.143
Refinement
*PLUS
Highest resolution: 1.5 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_angle_deg / Dev ideal: 2.1

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