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- PDB-7l3d: T4 Lysozyme L99A - 3-iodotoluene - RT -

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Basic information

Entry
Database: PDB / ID: 7l3d
TitleT4 Lysozyme L99A - 3-iodotoluene - RT
ComponentsEndolysin
KeywordsHYDROLASE / RT / 3-iodotoluene / 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
BETA-MERCAPTOETHANOL / 1-iodo-3-methylbenzene / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 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

Downloads & links

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Assembly

Deposited unit
A: Endolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1526
Polymers18,6201
Non-polymers5325
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-3 kcal/mol
Surface area8580 Å2
Unit cell
Length a, b, c (Å)61.130, 61.130, 97.749
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-302-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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

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Non-polymers , 5 types, 103 molecules

#2: 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
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-XQJ / 1-iodo-3-methylbenzene / 3-iodotoluene


Mass: 218.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H7I / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.56 %
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: 278 K / Ambient temp details: RT / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→52.94 Å / Num. obs: 46564 / % possible obs: 99.1 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Net I/σ(I): 11.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsDiffraction-ID% possible all
1.35-1.396.70.9152304199
6.04-52.946.20.0512520199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.12 Å52.94 Å

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Processing

Software
NameVersionClassification
xia2data scaling
PHASER2.8.2phasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4w51

4w51


Resolution: 1.35→46.552 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 17.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1621 2349 5.11 %
Rwork0.1443 43658 -
obs0.1452 46007 97.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.73 Å2 / Biso mean: 21.7656 Å2 / Biso min: 11.02 Å2
Refinement stepCycle: final / Resolution: 1.35→46.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 25 100 1414
Biso mean--32.45 36.79 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051501
X-RAY DIFFRACTIONf_angle_d0.7122035
X-RAY DIFFRACTIONf_dihedral_angle_d19.172583
X-RAY DIFFRACTIONf_chiral_restr0.061218
X-RAY DIFFRACTIONf_plane_restr0.004268
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.35-1.37750.3171110.3105248995
1.3775-1.40740.34581210.2995248896
1.4074-1.44020.28371400.2781247995
1.4402-1.47620.29751430.2467245696
1.4762-1.51610.24961420.2033252697
1.5161-1.56070.21691400.1718252698
1.5607-1.61110.20141220.1497259698
1.6111-1.66870.16731560.1373251898
1.6687-1.73550.15741280.126261599
1.7355-1.81450.15581660.1207252499
1.8145-1.91020.1441300.1142262299
1.9102-2.02990.15651240.1118253996
2.0299-2.18660.13711310.1077261999
2.1866-2.40660.13381520.11822611100
2.4066-2.75480.15991480.13592646100
2.7548-3.47060.1481590.1373263999
3.4706-46.5520.1431360.1512276597

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