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- PDB-7d2a: CBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid -

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Basic information

Entry
Database: PDB / ID: 7d2a
TitleCBM32 of AlyQ in complex with 4,5-unsaturated mannuronic acid
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-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesPersicobacter sp. CCB-QB2 (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.57 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

Downloads & links

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Assembly

Deposited unit
A: AlyQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7055
Polymers16,0951
Non-polymers6104
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area5870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.608, 55.773, 58.427
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 2 molecules A

#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: Polysaccharide 4-deoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-4)-alpha-L-gulopyranuronic acid


Type: oligosaccharide / Mass: 352.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
WURCS=2.0/2,2,1/[a1121A-1a_1-5][a11eEA-1a_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-L-GulpA]{[(4+1)][a-L-4-deoxy-AllpA]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 163 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 2.21 Å3/Da / Density % sol: 44.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M sodium HEPES, 2% PEG 400, 2.0M ammonium sulphate, 10mg/ml enzymatically degraded sodium alginate

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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 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.57→40.34 Å / Num. obs: 18779 / % possible obs: 91.5 % / Redundancy: 6.73 % / Rmerge(I) obs: 0.043 / Rrim(I) all: 0.046 / Χ2: 0.95 / Net I/σ(I): 22.2
Reflection shellResolution: 1.57→1.63 Å / Redundancy: 5.97 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 6.9 / Num. unique obs: 1284 / Rrim(I) all: 0.223 / Χ2: 1.19 / % possible all: 63.6

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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: 1.57→40.34 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.107 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.084 / ESU R Free: 0.083
RfactorNum. reflection% reflection
Rfree0.1945 901 4.802 %
Rwork0.1682 17862 -
all0.169 --
obs-18763 91.433 %
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: 14.486 Å2
Baniso -1Baniso -2Baniso -3
1--0.421 Å2-0 Å2-0 Å2
2--0.106 Å20 Å2
3---0.315 Å2
Refinement stepCycle: LAST / Resolution: 1.57→40.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms969 0 39 160 1168
LS refinement shellResolution: 1.57→1.611 Å
RfactorNum. reflection% reflection
Rfree0.345 43 -
Rwork0.257 863 -
obs--60.4806 %

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