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- PDB-6l00: Crystal structure of the cell-wall binding domain (CBD) of endoly... -

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Basic information

Entry
Database: PDB / ID: 6l00
TitleCrystal structure of the cell-wall binding domain (CBD) of endolysin LysIME-EF1
ComponentsLysin
KeywordsLYASE
Function / homologyCHAP domain profile. / CHAP domain / CHAP domain / symbiont-mediated cytolysis of host cell / Papain-like cysteine peptidase superfamily / metal ion binding / Lysin
Function and homology information
Biological speciesEnterococcus phage IMEEF1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsOuyang, S.Y. / Zhen, X.K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31800159 China
National Natural Science Foundation of China31770948 China
CitationJournal: Plos Pathog. / Year: 2020
Title: Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage.
Authors: Zhou, B. / Zhen, X. / Zhou, H. / Zhao, F. / Fan, C. / Perculija, V. / Tong, Y. / Mi, Z. / Ouyang, S.
History
DepositionSep 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysin


Theoretical massNumber of molelcules
Total (without water)8,1661
Polymers8,1661
Non-polymers00
Water95553
1
A: Lysin

A: Lysin

A: Lysin

A: Lysin


Theoretical massNumber of molelcules
Total (without water)32,6664
Polymers32,6664
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area5280 Å2
ΔGint-55 kcal/mol
Surface area13390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.880, 59.880, 87.010
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Lysin


Mass: 8166.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus phage IMEEF1 (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: S5MRN1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / Source method: isolated from a natural source / Formula: H2O

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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: 2.39 Å3/Da / Density % sol: 48.49 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7 / Details: 20% PEG 4000, 0.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 20, 2018
RadiationMonochromator: SSRF BEAMLINE BL17U1 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.75→49.33 Å / Num. obs: 8236 / % possible obs: 99 % / Redundancy: 9.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.089 / Rsym value: 0.091 / Net I/σ(I): 2.3
Reflection shellResolution: 1.75→1.813 Å / Num. unique obs: 552 / CC1/2: 0.696
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IST

6ist


Resolution: 1.75→42.342 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 27.75
RfactorNum. reflection% reflection
Rfree0.2438 814 9.89 %
Rwork0.2231 --
obs0.2251 8231 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 57.43 Å2 / Biso mean: 27.2266 Å2 / Biso min: 15.95 Å2
Refinement stepCycle: final / Resolution: 1.75→42.342 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms566 0 0 53 619
Biso mean---34.05 -
Num. residues----70

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