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- PDB-7loa: T4 lysozyme mutant L99A in complex with 3-fluoroiodobenzene -

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Basic information

Entry
Database: PDB / ID: 7loa
TitleT4 lysozyme mutant L99A in complex with 3-fluoroiodobenzene
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
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
BETA-MERCAPTOETHANOL / 1-fluoranyl-3-iodanyl-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
DepositionFeb 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 8, 2021Group: Database references / Category: citation / citation_author / database_2
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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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)20,2706
Polymers19,6921
Non-polymers5795
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.057, 60.057, 96.276
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 / Endolysin / Lysis protein / Muramidase


Mass: 19691.541 Da / Num. of mol.: 1
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-Y7V / 1-fluoranyl-3-iodanyl-benzene


Mass: 221.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4FI / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 3 / 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: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 51.68 %
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→52.011 Å / Num. obs: 88670 / % possible obs: 99.5 % / Redundancy: 18.7 % / Biso Wilson estimate: 13.48 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.013 / Rrim(I) all: 0.055 / Net I/σ(I): 23.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.07-1.0912.32.73241930.3670.7932.85196.5
5.86-52.01117.60.02364710.0050.02399.9

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Phasing

PhasingMethod: molecular replacement

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Processing

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

4w57


Resolution: 1.07→52.01 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2186 4481 5.06 %
Rwork0.212 84128 -
obs0.2124 88609 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.53 Å2 / Biso mean: 16.6937 Å2 / Biso min: 6.34 Å2
Refinement stepCycle: final / Resolution: 1.07→52.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 28 122 1447
Biso mean--24.88 23.96 -
Num. residues----164
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051403
X-RAY DIFFRACTIONf_angle_d0.7491885
X-RAY DIFFRACTIONf_chiral_restr0.06207
X-RAY DIFFRACTIONf_plane_restr0.004240
X-RAY DIFFRACTIONf_dihedral_angle_d2.2911450
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.07-1.08220.32131360.3388268796
1.0822-1.09490.32191430.3206269997
1.0949-1.10830.30471560.2957270898
1.1083-1.12230.31381700.281272199
1.1223-1.13710.29411750.2736271499
1.1371-1.15260.26491530.2697280799
1.1526-1.16910.2861460.2553275299
1.1691-1.18660.28611560.2582274899
1.1866-1.20510.27861470.245277999
1.2051-1.22490.21751090.24242837100
1.2249-1.2460.27241640.24312779100
1.246-1.26870.23141590.2399274499
1.2687-1.29310.2331280.22632822100
1.2931-1.31940.24481720.23082760100
1.3194-1.34810.25861380.2262827100
1.3481-1.37950.24851600.22662786100
1.3795-1.4140.26921560.22812775100
1.414-1.45220.24341450.22372818100
1.4522-1.4950.22341380.21992836100
1.495-1.54320.21671270.20782824100
1.5432-1.59840.20981410.21222826100
1.5984-1.66240.22911540.21712813100
1.6624-1.73810.26641300.21422855100
1.7381-1.82970.21971580.20782817100
1.8297-1.94430.1961420.2082863100
1.9443-2.09450.18121440.19992840100
2.0945-2.30520.19841760.18582859100
2.3052-2.63880.2351520.20932860100
2.6388-3.32450.20811460.2132936100
3.3245-52.010.1941600.19373036100

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