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- PDB-7l38: T4 Lysozyme L99A - Apo - cryo -

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Basic information

Entry
Database: PDB / ID: 7l38
TitleT4 Lysozyme L99A - Apo - cryo
ComponentsEndolysin
KeywordsHYDROLASE / cryo / 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
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 / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.33 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
Water2,288127
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area890 Å2
ΔGint-3 kcal/mol
Surface area8530 Å2
Unit cell
Length a, b, c (Å)59.835, 59.835, 96.334
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 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-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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.67 Å3/Da / Density % sol: 53.99 %
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: Jul 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.33→51.82 Å / Num. obs: 46473 / % possible obs: 99.9 % / Redundancy: 6 % / CC1/2: 0.995 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1
Reflection shellResolution: 1.33→1.35 Å / Num. unique obs: 2270 / CC1/2: 0.867

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.92 Å51.82 Å
Translation4.92 Å51.82 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: 1.33→51.819 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 25.21 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1995 2347 5.1 %
Rwork0.1782 43714 -
obs0.1793 46061 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.66 Å2 / Biso mean: 26.3494 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 1.33→51.819 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 21 129 1439
Biso mean--33.52 35.16 -
Num. residues----162
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051407
X-RAY DIFFRACTIONf_angle_d0.7151899
X-RAY DIFFRACTIONf_dihedral_angle_d15.078549
X-RAY DIFFRACTIONf_chiral_restr0.063206
X-RAY DIFFRACTIONf_plane_restr0.004246
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3301-1.35730.30551020.342256099
1.3573-1.38680.38111350.3169252599
1.3868-1.4190.31361440.2826253199
1.419-1.45450.32931440.2454251999
1.4545-1.49390.29351440.2323253699
1.4939-1.53780.23661310.1878255299
1.5378-1.58750.24061300.1762551100
1.5875-1.64420.26731470.16182571100
1.6442-1.710.21431440.1562255499
1.71-1.78790.17851410.14762563100
1.7879-1.88210.20371410.15642563100
1.8821-2.00010.20581200.15652613100
2.0001-2.15450.18141280.15052602100
2.1545-2.37130.18281580.1552584100
2.3713-2.71440.23191410.16932635100
2.7144-3.41980.17731650.18052634100
3.4198-51.8190.17081320.1846262194

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