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- PDB-7jrl: The structure of CBM51-2 in complex with GlcNAc and INT domains f... -

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Basic information

Entry
Database: PDB / ID: 7jrl
TitleThe structure of CBM51-2 in complex with GlcNAc and INT domains from Clostridium perfringens ZmpB
ComponentsF5/8 type C domain proteinDiscoidin domain
KeywordsSUGAR BINDING PROTEIN / Carbohydrate binding module
Function / homology
Function and homology information


hydrolase activity, acting on glycosyl bonds / metabolic process / 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 / Leucine-rich repeat domain superfamily / Galactose-binding-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
PHOSPHATE ION / F5/8 type C domain protein
Similarity search - Component
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 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 12, 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)54,3199
Polymers53,5931
Non-polymers7278
Water9,854547
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-4 kcal/mol
Surface area24100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.120, 51.360, 78.190
Angle α, β, γ (deg.)90.000, 115.470, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Sugars , 2 types, 2 molecules A

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


Mass: 53592.801 Da / Num. of mol.: 1
Fragment: Carbohydrate binding module (UNP residues 1227-1687)
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
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 5 types, 554 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 547 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.15 M sodium phosphate monobasic, 18% PEG3350, 0.1 M Tris-HCl

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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: Liquid nitrogen-cooled 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: 1.5→42.86 Å / Num. obs: 86269 / % possible obs: 100 % / Redundancy: 5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.082 / Rpim(I) all: 0.04 / Net I/σ(I): 13.2
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 3.6 / Num. unique obs: 12539 / CC1/2: 0.735 / Rpim(I) all: 0.283 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.8.0258refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2VMG

2vmg


Resolution: 1.5→38.93 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.951 / SU B: 1.147 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.071 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 4306 5 %RANDOM
Rwork0.1833 ---
obs0.1839 81962 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 62.74 Å2 / Biso mean: 16.24 Å2 / Biso min: 6.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å2-0.11 Å2
2--0.26 Å20 Å2
3----0.38 Å2
Refinement stepCycle: final / Resolution: 1.5→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3556 0 53 548 4157
Biso mean--18.93 23.32 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0123664
X-RAY DIFFRACTIONr_angle_refined_deg1.2291.6384944
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5415464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.54925.47181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97515687
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1481512
X-RAY DIFFRACTIONr_chiral_restr0.0840.2493
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022696
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 338 -
Rwork0.22 5990 -
all-6328 -
obs--100 %

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