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- PDB-1pqk: Repacking of the Core of T4 Lysozyme by Automated Design -

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Basic information

Entry
Database: PDB / ID: 1pqk
TitleRepacking of the Core of T4 Lysozyme by Automated Design
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: 2 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
DepositionJun 18, 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
B: Lysozyme
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)56,1193
Polymers56,1193
Non-polymers00
Water6,341352
1
A: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,7061
Polymers18,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,7061
Polymers18,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lysozyme


Theoretical massNumber of molelcules
Total (without water)18,7061
Polymers18,7061
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.230, 67.280, 61.650
Angle α, β, γ (deg.)90.00, 112.43, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 18706.410 Da / Num. of mol.: 3
Mutation: C54T, G77A, I78V, C97A, L118I, M120Y, L133F, V149I, T152V
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: 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.: 352 / 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: 2.67 Å3/Da / Density % sol: 53.9 %
Crystal growTemperature: 277 K / pH: 6.7
Details: Potassium phosphate, sodium PHOSPHATE, NaCl, BME, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 6.70
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
125 %PEG34001reservoir
25 %PEG6001reservoir
3200 mM1reservoirNaCl
4100 mMsodium potassium phosphate1reservoirpH6.7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2→23.702 Å / Num. obs: 40412 / % possible obs: 96 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 20.378 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 12.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.188 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.188 / % possible all: 95.2
Reflection
*PLUS
Highest resolution: 2 Å
Reflection shell
*PLUS
% possible obs: 91 %

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
TNTrefinement
CCP4(SCALA)data scaling
TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→72.5 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.277 986 0.02 %RANDOM
Rwork0.177 ---
all0.18 38780 --
obs0.18 38780 --
Solvent computationSolvent model: TNT / Bsol: 292.675 Å2 / ksol: 0.93407 e/Å3
Refinement stepCycle: LAST / Resolution: 2→72.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3956 0 0 352 4308
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.184
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 2 Å / Rfactor Rwork: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.02
X-RAY DIFFRACTIONt_angle_deg2.9

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