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- PDB-7l3a: T4 Lysozyme L99A - toluene - cryo -

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Basic information

Entry
Database: PDB / ID: 7l3a
TitleT4 Lysozyme L99A - toluene - cryo
ComponentsEndolysin
KeywordsHYDROLASE / cryo / toluene / L99A
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 / molecular replacement / Resolution: 1.11 Å
AuthorsFischer, M. / Bradford, S.Y.C.
CitationJournal: Chem Sci / Year: 2021
Title: Temperature artifacts in protein structures bias ligand-binding predictions.
Authors: Bradford, S.Y.C. / El Khoury, L. / Ge, Y. / Osato, M. / Mobley, D.L. / Fischer, M.
History
DepositionDec 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 27, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7132
Polymers18,6201
Non-polymers921
Water2,972165
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area340 Å2
ΔGint3 kcal/mol
Surface area8640 Å2
Unit cell
Length a, b, c (Å)59.907, 59.907, 96.255
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

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


Mass: 18620.387 Da / Num. of mol.: 1 / Mutation: R12G/I137R/L99A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.68 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris- ...Details: Crystals were grown from a 10 mg/mL frozen protein solution by the hanging drop method at 291-293K, with a 1:1 drop ratio of protein to solution and over a well solution of 0.1 M Tris-hydrochloride (pH 8), 20%-26% (w/v) PEG 4000, 70-170 mM lithium citrate, 8%-18% 2-propanol, 50 mM 2-mercaptoethanol, and 50 mM 2-hydroxyethyl disulfide
Temp details: 291-293

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.11→45.67 Å / Num. obs: 74260 / % possible obs: 96 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.13-1.163.90.6422519170.6
5.05-45.669.50.0284043199.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.06 Å45.67 Å
Translation5.06 Å45.67 Å

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Processing

Software
NameVersionClassification
xia2data scaling
PHASER2.8.0phasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w51

4w51


Resolution: 1.11→45.67 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2032 1993 2.68 %
Rwork0.1835 72267 -
obs0.1841 74260 93.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 50.46 Å2 / Biso mean: 15.9005 Å2 / Biso min: 8.97 Å2
Refinement stepCycle: final / Resolution: 1.11→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 14 168 1471
Biso mean--15.27 26.1 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041438
X-RAY DIFFRACTIONf_angle_d0.7871939
X-RAY DIFFRACTIONf_dihedral_angle_d13.808541
X-RAY DIFFRACTIONf_chiral_restr0.063211
X-RAY DIFFRACTIONf_plane_restr0.005252
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1101-1.13780.3915930.3561322360
1.1378-1.16860.3851080.3327397573
1.1686-1.2030.36711350.2915461985
1.203-1.24180.30251390.2586514694
1.2418-1.28620.23391500.2212542799
1.2862-1.33770.2341510.2043539899
1.3377-1.39860.18671490.18025493100
1.3986-1.47230.1991490.1726544099
1.4723-1.56460.17891470.14585480100
1.5646-1.68540.16261550.14645538100
1.6854-1.8550.18451490.15195529100
1.855-2.12340.17351520.15375557100
2.1234-2.67520.17441530.16835608100
2.6752-45.670.20691630.19085834100

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