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- PDB-7jnb: The structure of CBM32-1 and CBM32-2 domains from Clostridium per... -

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Basic information

Entry
Database: PDB / ID: 7jnb
TitleThe structure of CBM32-1 and CBM32-2 domains from Clostridium perfringens ZmpB in complex with GalNAc
ComponentsF5/8 type C domain protein
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding module
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 / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / Peptidase family M60 domain / Peptidase M60, enhancin-like domain 3 / Peptidase M60, enhancin and enhancin-like / Peptidase family M60 domain profile. ...Glycosyl hydrolase family 98, putative carbohydrate-binding module / NPCBM domain superfamily / NPCBM/NEW2 domain / NPCBM / Pesticidal crystal protein Cry22Aa, Ig-like domain / Bacterial surface protein, Ig-like domain / 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 / 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
2-acetamido-2-deoxy-alpha-D-galactopyranose / F5/8 type C domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / molecular replacement / Resolution: 2 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
DepositionAug 4, 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 30, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)52,2356
Polymers51,7501
Non-polymers4865
Water4,648258
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area750 Å2
ΔGint5 kcal/mol
Surface area18100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.610, 89.610, 185.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein F5/8 type C domain protein


Mass: 51749.738 Da / Num. of mol.: 1 / Fragment: Carbohydrate binding module (UNP residues 28-453)
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
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 258 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 66.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 1.6 M tribasic ammonium citrate, 3% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91966 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 11, 2011
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91966 Å / Relative weight: 1
ReflectionResolution: 2→46.51 Å / Num. obs: 50493 / % possible obs: 97.2 % / Redundancy: 8.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.038 / Net I/σ(I): 11.4
Reflection shellResolution: 2→2.11 Å / Redundancy: 8.4 % / Rmerge(I) obs: 1.017 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 7126 / CC1/2: 0.605 / Rpim(I) all: 0.341 / % possible all: 95.7

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Phasing

Phasing
Method
SAD
molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
SHARPphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SAD / Resolution: 2→46.51 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.935 / SU B: 3.718 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2349 2573 5.1 %RANDOM
Rwork0.2092 ---
obs0.2105 47838 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 84.07 Å2 / Biso mean: 36.471 Å2 / Biso min: 16.76 Å2
Baniso -1Baniso -2Baniso -3
1--0.47 Å20 Å20 Å2
2---0.47 Å20 Å2
3---0.93 Å2
Refinement stepCycle: final / Resolution: 2→46.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3175 0 29 258 3462
Biso mean--39.04 39.96 -
Num. residues----395
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0123261
X-RAY DIFFRACTIONr_angle_refined_deg1.021.6514394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2545392
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.32523.969194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.415551
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7211516
X-RAY DIFFRACTIONr_chiral_restr0.080.2424
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022529
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 185 -
Rwork0.298 3411 -
all-3596 -
obs--95.23 %

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