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- PDB-7lxa: T4 lysozyme mutant L99A -

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Basic information

Entry
Database: PDB / ID: 7lxa
TitleT4 lysozyme mutant L99A
ComponentsLysozyme
KeywordsPROTEIN BINDING / HYDROLASE / mutant / lysozyme / small molecule / L99A / complex
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
Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme-like domain superfamily
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / (2-methylprop-2-en-1-yl)benzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.07 Å
AuthorsKamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Energy penalties enhance flexible receptor docking in a model cavity.
Authors: Kamenik, A.S. / Singh, I. / Lak, P. / Balius, T.E. / Liedl, K.R. / Shoichet, B.K.
History
DepositionMar 3, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 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

Downloads & links

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Assembly

Deposited unit
A: Lysozyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0244
Polymers19,6921
Non-polymers3323
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.154, 60.154, 96.293
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 / Endolysin / Muramidase


Mass: 19691.541 Da / Num. of mol.: 1 / Mutation: L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: e, T4Tp126
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: D9IEF7, lysozyme
#2: Chemical ChemComp-YGS / (2-methylprop-2-en-1-yl)benzene


Mass: 132.202 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H12 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.55 Å3/Da / Density % sol: 51.84 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Isopropanol, PEG 4000, Tris-Cl pH 8.0, Beta-mercaptoethanol, 2-hyrdoxyethyl disulfide

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.95386 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 24, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95386 Å / Relative weight: 1
ReflectionResolution: 1.07→52.1 Å / Num. obs: 89360 / % possible obs: 99.9 % / Redundancy: 18.4 % / Biso Wilson estimate: 14.19 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.016 / Rrim(I) all: 0.07 / Net I/σ(I): 15.1 / Num. measured all: 1641804 / Scaling rejects: 46
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.07-1.0911.93.3145127343030.3460.9853.4650.898.2
5.86-52.118.20.037116806430.9990.0090.03858.199.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.11.1_2575refinement
XDSdata reduction
Aimless0.5.32data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W57

4w57


Resolution: 1.07→52.095 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.211 4517 5.06 %
Rwork0.2052 84669 -
obs0.2055 89186 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 35.47 Å2 / Biso mean: 17.0114 Å2 / Biso min: 10.31 Å2
Refinement stepCycle: final / Resolution: 1.07→52.095 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1252 0 22 112 1386
Biso mean--20.59 24 -
Num. residues----160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041349
X-RAY DIFFRACTIONf_angle_d0.7691817
X-RAY DIFFRACTIONf_chiral_restr0.06200
X-RAY DIFFRACTIONf_plane_restr0.005233
X-RAY DIFFRACTIONf_dihedral_angle_d2.1011109
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.07-1.08220.3581390.3692270496
1.0822-1.09490.32161450.3417276199
1.0949-1.10820.33431670.30992776100
1.1082-1.12230.27511650.28832738100
1.1223-1.1370.28261870.27692806100
1.137-1.15260.28171650.26412737100
1.1526-1.16910.25361400.25452820100
1.1691-1.18650.27821590.24352771100
1.1865-1.20510.22161480.22832824100
1.2051-1.22480.21691090.23542855100
1.2248-1.2460.23061550.22452778100
1.246-1.26860.23021710.21452779100
1.2686-1.2930.22161170.21072836100
1.293-1.31940.22121760.21552803100
1.3194-1.34810.21581300.20222796100
1.3481-1.37950.22891680.20352793100
1.3795-1.4140.22441620.20342791100
1.414-1.45220.23451450.19982837100
1.4522-1.49490.20971370.19332834100
1.4949-1.54320.18831270.19222879100
1.5432-1.59840.19881390.18712804100
1.5984-1.66240.20431550.19242825100
1.6624-1.7380.18981280.19222856100
1.738-1.82970.20391610.19292847100
1.8297-1.94430.18911440.19772850100
1.9443-2.09440.1861410.19512854100
2.0944-2.30520.19261770.19072858100
2.3052-2.63870.22281540.20772888100
2.6387-3.32450.21721440.20632937100
3.3245-52.0950.20111620.20023032100

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