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- PDB-7loc: T4 lysozyme mutant L99A in complex with 1-bromanyl-4-fluoranyl-benzene -

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Basic information

Entry
Database: PDB / ID: 7loc
TitleT4 lysozyme mutant L99A in complex with 1-bromanyl-4-fluoranyl-benzene
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-bromanyl-4-fluoranyl-benzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.16 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)20,1455
Polymers19,6921
Non-polymers4534
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.266, 60.266, 96.411
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 / 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-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#3: 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
#4: Chemical ChemComp-Y87 / 1-bromanyl-4-fluoranyl-benzene


Mass: 174.998 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H4BrF / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.57 Å3/Da / Density % sol: 52.08 %
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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95386 Å / Relative weight: 1
ReflectionResolution: 1.16→52.192 Å / Num. obs: 70492 / % possible obs: 99.7 % / Redundancy: 19.3 % / Biso Wilson estimate: 12.99 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Net I/σ(I): 24.2
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
1.16-1.1817.61.9765707732360.6710.4722.0341.794
6.36-52.1917.70.021918451910.0050.022112.8100

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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: 1.16→52.192 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 3528 5.01 %
Rwork0.1976 66896 -
obs0.1981 70424 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.51 Å2 / Biso mean: 16.0186 Å2 / Biso min: 8.1 Å2
Refinement stepCycle: final / Resolution: 1.16→52.192 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1290 0 24 124 1438
Biso mean--24.03 22.91 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041390
X-RAY DIFFRACTIONf_angle_d0.7651867
X-RAY DIFFRACTIONf_chiral_restr0.063204
X-RAY DIFFRACTIONf_plane_restr0.005236
X-RAY DIFFRACTIONf_dihedral_angle_d2.041442
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.1604-1.17630.28791090.2844242092
1.1763-1.19310.28591520.27742638100
1.1931-1.21090.271490.25992671100
1.2109-1.22980.24821350.24942668100
1.2298-1.250.31051440.24062625100
1.25-1.27150.23351470.23472646100
1.2715-1.29460.19791220.22632676100
1.2946-1.31950.27961070.21812682100
1.3195-1.34650.22911270.21052653100
1.3465-1.37580.23851310.2092698100
1.3758-1.40780.22031250.20922668100
1.4078-1.4430.20921610.20132665100
1.443-1.4820.2021520.19552637100
1.482-1.52560.1861650.18632647100
1.5256-1.57480.22251370.18692693100
1.5748-1.63110.19621470.17732673100
1.6311-1.69640.19991430.18612669100
1.6964-1.77370.18381390.18552720100
1.7737-1.86720.20231540.18492652100
1.8672-1.98420.19611360.19142688100
1.9842-2.13740.1871550.18432700100
2.1374-2.35250.20061320.18462719100
2.3525-2.69280.21051450.2012740100
2.6928-3.39260.23631500.2032763100
3.3926-52.1920.18691640.18692885100

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