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- PDB-7vbo: Alginate binding domain CBM -

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Basic information

Entry
Database: PDB / ID: 7vbo
TitleAlginate binding domain CBM
ComponentsAlginate lyase
KeywordsSUGAR BINDING PROTEIN / beta sandwich
Function / homology
Function and homology information


mannuronate-specific alginate lyase / poly(beta-D-mannuronate) lyase activity / hydrolase activity, acting on glycosyl bonds / metabolic process / carbohydrate binding / metal ion binding
Similarity search - Function
Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain ...Heparinase II, N-terminal / Domain of unknown function (DUF4962) / Heparinase II/III-like / Heparinase II/III-like protein / Chondroitin AC/alginate lyase / CBM6 (carbohydrate binding type-6) domain profile. / Carbohydrate binding module family 6 / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Galactose-binding-like domain superfamily / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesDefluviitalea phaphyphila (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsJi, S.Q. / She, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31670001 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Identification and structural analysis of a carbohydrate-binding module specific to alginate, a representative of a new family, CBM96.
Authors: Ji, S. / Tian, X. / Li, X. / She, Q.
History
DepositionSep 1, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 7, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2023Group: Database references / Category: citation / citation_author
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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alginate lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8463
Polymers22,7091
Non-polymers1362
Water2,612145
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area8440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.587, 92.584, 122.263
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-380-

HOH

21A-417-

HOH

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Components

#1: Protein Alginate lyase


Mass: 22709.494 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Defluviitalea phaphyphila (bacteria) / Gene: Dp0100 / Plasmid: pEasy E1 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A4Y5UXE1, mannuronate-specific alginate lyase
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / Source method: isolated from a natural source / Formula: H2O
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: 2.12 Å3/Da / Density % sol: 37.5 % / Mosaicity: 0.14 °
Crystal growTemperature: 298 K / Method: evaporation / pH: 8 / Details: 1.8 M lithium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97928 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.35→46.33 Å / Num. obs: 37994 / % possible obs: 99.3 % / Redundancy: 12.8 % / CC1/2: 1 / Rmerge(I) obs: 0.051 / Rpim(I) all: 0.014 / Rrim(I) all: 0.053 / Net I/σ(I): 35
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.35-1.537.90.294974012260.9650.1030.3135.186.9
8.23-19.4712.10.04523781970.9990.0130.04780.792.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
CRANK2phasing
RefinementMethod to determine structure: SAD / Resolution: 1.5→46.33 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.964 / SU B: 0.862 / SU ML: 0.036 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.054 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1943 1442 5 %RANDOM
Rwork0.1802 ---
obs0.1809 37994 99.06 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.13 Å2 / Biso mean: 20.098 Å2 / Biso min: 10.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2--0.75 Å20 Å2
3----0.8 Å2
Refinement stepCycle: final / Resolution: 1.5→46.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1429 0 6 145 1580
Biso mean--36.94 28.56 -
Num. residues----182
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0131463
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181309
X-RAY DIFFRACTIONr_angle_refined_deg1.8711.6441986
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5913046
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9895181
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.14625.83372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07515245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.897152
X-RAY DIFFRACTIONr_chiral_restr0.0930.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021664
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
LS refinement shellResolution: 1.5→1.5 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.3 147 -
Rwork0.255 2796 -
obs--99.53 %

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