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- PDB-6ujf: Crystal structure of the Clostridial cellulose synthase subunit Z... -

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Basic information

Entry
Database: PDB / ID: 6ujf
TitleCrystal structure of the Clostridial cellulose synthase subunit Z (CcsZ) from Clostridioides difficile
ComponentsEndoglucanase
KeywordsHYDROLASE / glycosyl / biofilm / cellulose / GH8
Function / homology: / cellulase / Glycoside hydrolase, family 5 / Cellulase (glycosyl hydrolase family 5) / cellulase activity / membrane => GO:0016020 / Glycoside hydrolase superfamily / beta-D-glucopyranose / Endoglucanase H
Function and homology information
Biological speciesClostridioides difficile (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsScott, W. / Lowrance, B. / Anderson, A.C. / Weadge, J.T.
Funding support Canada, 1items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)229971 Canada
CitationJournal: Plos One / Year: 2020
Title: Identification of the Clostridial cellulose synthase and characterization of the cognate glycosyl hydrolase, CcsZ.
Authors: Scott, W. / Lowrance, B. / Anderson, A.C. / Weadge, J.T.
History
DepositionOct 3, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 9, 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 / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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: Endoglucanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5512
Polymers38,3711
Non-polymers1801
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Protein purifies as a monomer by gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.020, 46.530, 61.090
Angle α, β, γ (deg.)90.000, 94.500, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Endoglucanase


Mass: 38371.230 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: celH, SAMEA1402348_00819 / Production host: Escherichia coli BL21 (bacteria) / Variant (production host): CodonPlus / References: UniProt: A0A5Q9L120*PLUS, cellulase
#2: Sugar ChemComp-BGC / beta-D-glucopyranose / beta-D-glucose / D-glucose / glucose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThere is no UniProt sequence available at the time of processing. The deposited sequence ...There is no UniProt sequence available at the time of processing. The deposited sequence corresponds to the GenBank entry WP_077724661.1.

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100 mM MES, 200 mM calcium acetate, 20% (v/v) poly(ethylene glycol) 8000, 2.5 mM cellotriose

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationMonochromator: ACCEL/BRUKER DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.9→31.692 Å / Num. obs: 25294 / % possible obs: 99.5 % / Redundancy: 2 % / Biso Wilson estimate: 48.53 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.01846 / Rpim(I) all: 0.01846 / Rrim(I) all: 0.02611 / Net I/σ(I): 17.96
Reflection shellResolution: 1.9→2.071 Å / Redundancy: 2 % / Rmerge(I) obs: 0.2836 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 2157 / CC1/2: 0.903 / Rpim(I) all: 0.2836 / Rrim(I) all: 0.4011 / % possible all: 99.58

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
MrBUMPphasing
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UJE

3uje


Resolution: 2→31.692 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 37.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2817 1089 5.01 %
Rwork0.2345 20656 -
obs0.2369 21745 99.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 86.87 Å2 / Biso mean: 44.2928 Å2 / Biso min: 21.23 Å2
Refinement stepCycle: final / Resolution: 2→31.692 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2550 0 12 82 2644
Biso mean--30 42.17 -
Num. residues----301
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.0910.40051360.37222569100
2.091-2.20120.39541350.32022570100
2.2012-2.33910.35351350.3233254499
2.3391-2.51970.36681330.2896254699
2.5197-2.77310.3881360.2986257699
2.7731-3.1740.35121360.26362571100
3.174-3.99770.26161370.21182604100
3.9977-31.6920.1951410.17242676100

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