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- PDB-7l37: T4 Lysozyme L99A - Apo - RT -

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Basic information

Entry
Database: PDB / ID: 7l37
TitleT4 Lysozyme L99A - Apo - RT
ComponentsEndolysin
KeywordsHYDROLASE / RTX / apo / 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
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 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.439 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)18,9345
Polymers18,6201
Non-polymers3144
Water1,26170
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-5 kcal/mol
Surface area8790 Å2
Unit cell
Length a, b, c (Å)61.006, 61.006, 98.529
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

#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-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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.84 Å3/Da / Density % sol: 56.73 % / Description: Diamond-shaped
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: 291-293K

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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 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.439→49.26 Å / Num. obs: 39149 / % possible obs: 99.9 % / Redundancy: 9.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.061 / Net I/σ(I): 15.5
Reflection shellResolution: 1.439→1.46 Å / Redundancy: 9 % / Rmerge(I) obs: 0.852 / Num. unique obs: 1868 / CC1/2: 0.545 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4W51

4w51


Resolution: 1.439→36.031 Å / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1845 1985 5.1 %
Rwork0.155 36925 -
obs0.1565 38910 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.43 Å2 / Biso mean: 25.8688 Å2 / Biso min: 14.25 Å2
Refinement stepCycle: final / Resolution: 1.439→36.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 21 72 1382
Biso mean--35.01 41.07 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051516
X-RAY DIFFRACTIONf_angle_d0.7412055
X-RAY DIFFRACTIONf_dihedral_angle_d16.831594
X-RAY DIFFRACTIONf_chiral_restr0.064220
X-RAY DIFFRACTIONf_plane_restr0.004271
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.439-1.47470.37271370.3519247495
1.4747-1.51460.32871280.2961259399
1.5146-1.55910.31881540.2513257399
1.5591-1.60950.26541500.2152628100
1.6095-1.6670.23771490.1788257799
1.667-1.73370.22011220.1502265899
1.7337-1.81260.16331320.13212611100
1.8126-1.90820.15471530.1152636100
1.9082-2.02770.151510.11232631100
2.0277-2.18430.13221410.09952647100
2.1843-2.4040.11921370.10852670100
2.404-2.75180.16361330.13052687100
2.7518-3.46660.17061390.15092703100
3.4666-36.0310.20431590.18022837100

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