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- PDB-7jfs: The structure of the CBM32-1, CBM32-2, and M60 catalytic domains ... -

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Basic information

Entry
Database: PDB / ID: 7jfs
TitleThe structure of the CBM32-1, CBM32-2, and M60 catalytic domains from Clostridium perfringens ZmpB
ComponentsF5/8 type C domain protein
KeywordsHYDROLASE / glycopeptidase
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metal ion binding
Similarity search - Function
Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Pesticidal crystal protein Cry22Aa, Ig-like domain ...Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. / Peptidase M60-like family / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Leucine-rich repeat profile. / Leucine-rich repeat / Galactose-binding-like domain superfamily / Leucine-rich repeat domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
F5/8 type C domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.6 Å
AuthorsPluvinage, B. / Boraston, A.B.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
Canadian Glycomics Network (GLYCONET) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Architecturally complex O -glycopeptidases are customized for mucin recognition and hydrolysis.
Authors: Pluvinage, B. / Ficko-Blean, E. / Noach, I. / Stuart, C. / Thompson, N. / McClure, H. / Buenbrazo, N. / Wakarchuk, W. / Boraston, A.B.
History
DepositionJul 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 18, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 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

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Assembly

Deposited unit
A: F5/8 type C domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,0742
Polymers112,0081
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-36 kcal/mol
Surface area44150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)185.743, 185.743, 81.591
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

#1: Protein F5/8 type C domain protein / Glycopeptidase


Mass: 112008.195 Da / Num. of mol.: 1 / Fragment: UNP residues 46-1003
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (strain ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A) (bacteria)
Strain: ATCC 13124 / DSM 756 / JCM 1290 / NCIMB 6125 / NCTC 8237 / Type A
Gene: CPF_1489 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2YN38, Hydrolases
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
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: 3.63 Å3/Da / Density % sol: 66.09 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 2% Tascimate, 0.1 M Bis-Tris, 15% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 4.6→30 Å / Num. obs: 9041 / % possible obs: 99.7 % / Redundancy: 4.7 % / CC1/2: 0.981 / Rmerge(I) obs: 0.183 / Rpim(I) all: 0.084 / Net I/σ(I): 8.6
Reflection shellResolution: 4.6→4.68 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.757 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 449 / CC1/2: 0.798 / Rpim(I) all: 0.387 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.18_3845refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5KDN

5kdn


Resolution: 4.6→29.93 Å / SU ML: 0.65 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.93 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3092 427 4.74 %
Rwork0.2609 8578 -
obs0.2633 9005 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 219.36 Å2 / Biso mean: 96.0881 Å2 / Biso min: 59.42 Å2
Refinement stepCycle: final / Resolution: 4.6→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7730 0 1 0 7731
Biso mean--129.09 --
Num. residues----958
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 3

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.6-5.270.3531200.30732837295799
5.27-6.620.37261440.303228512995100
6.62-29.930.25111630.1992890305399

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