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- PDB-7d29: CBM32 of AlyQ -

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Basic information

Entry
Database: PDB / ID: 7d29
TitleCBM32 of AlyQ
ComponentsAlyQ
KeywordsSUGAR BINDING PROTEIN / CBM32 / alginate
Function / homology
Function and homology information


hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Alginate lyase 2 / Alginate lyase / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPersicobacter sp. CCB-QB2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsTeh, A.H. / Sim, P.F.
Funding support Malaysia, 1items
OrganizationGrant numberCountry
Other government Malaysia
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis for binding uronic acids by family 32 carbohydrate-binding modules.
Authors: Teh, A.H. / Sim, P.F. / Hisano, T.
History
DepositionSep 16, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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: AlyQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1352
Polymers16,0951
Non-polymers401
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.447, 55.670, 58.496
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AlyQ


Mass: 16095.180 Da / Num. of mol.: 1 / Fragment: CBM32
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Persicobacter sp. CCB-QB2 (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A3B6UEP6
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O
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: 2.2 Å3/Da / Density % sol: 44.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M sodium HEPES, 20% PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.7→29.56 Å / Num. obs: 14744 / % possible obs: 91.2 % / Redundancy: 3.15 % / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.027 / Χ2: 0.95 / Net I/σ(I): 33.3
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.84 % / Rmerge(I) obs: 0.066 / Mean I/σ(I) obs: 13.2 / Num. unique obs: 969 / Rrim(I) all: 0.081 / Χ2: 0.97 / % possible all: 61

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
CrystalCleardata reduction
CrystalCleardata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5XNR

5xnr


Resolution: 1.7→22.252 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.952 / SU B: 1.455 / SU ML: 0.049 / Cross valid method: FREE R-VALUE / ESU R: 0.097 / ESU R Free: 0.097
RfactorNum. reflection% reflection
Rfree0.1893 682 4.626 %
Rwork0.1546 14062 -
all0.156 --
obs-14744 91.097 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 12.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.048 Å2-0 Å2-0 Å2
2---0.08 Å20 Å2
3---0.128 Å2
Refinement stepCycle: LAST / Resolution: 1.7→22.252 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1003 0 1 142 1146
LS refinement shellResolution: 1.7→1.744 Å
RfactorNum. reflection% reflection
Rfree0.258 34 -
Rwork0.194 642 -
obs--56.9503 %

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