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- PDB-7vqm: GH2 beta-galacturonate AqGalA in complex with galacturonide -

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Basic information

Entry
Database: PDB / ID: 7vqm
TitleGH2 beta-galacturonate AqGalA in complex with galacturonide
ComponentsGH2 beta-galacturonate AqGalA
KeywordsHYDROLASE / beta-Galacturonate / Complex
Function / homology
Function and homology information


Galactose-binding domain-like / Glycosidases / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-galactopyranuronic acid
Similarity search - Component
Biological speciesAquimarina sp. (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYang, J.
Funding support China, 1items
OrganizationGrant numberCountry
Other governmentZDKJ202018 China
CitationJournal: Appl.Environ.Microbiol. / Year: 2022
Title: Structural and Biochemical Basis of a Marine Bacterial Glycoside Hydrolase Family 2 beta-Glycosidase with Broad Substrate Specificity
Authors: Yang, J. / Li, S. / Liu, Y. / Li, R. / Long, L.
History
DepositionOct 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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

Downloads & links

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Assembly

Deposited unit
A: GH2 beta-galacturonate AqGalA
B: GH2 beta-galacturonate AqGalA
C: GH2 beta-galacturonate AqGalA
D: GH2 beta-galacturonate AqGalA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,64312
Polymers284,7254
Non-polymers9188
Water22,8071266
1
A: GH2 beta-galacturonate AqGalA
B: GH2 beta-galacturonate AqGalA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8226
Polymers142,3632
Non-polymers4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6570 Å2
ΔGint-36 kcal/mol
Surface area42100 Å2
MethodPISA
2
C: GH2 beta-galacturonate AqGalA
D: GH2 beta-galacturonate AqGalA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,8226
Polymers142,3632
Non-polymers4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6600 Å2
ΔGint-36 kcal/mol
Surface area42060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.413, 154.006, 115.925
Angle α, β, γ (deg.)90.000, 109.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
GH2 beta-galacturonate AqGalA


Mass: 71181.258 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquimarina sp. (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Sugar
ChemComp-GTR / beta-D-galactopyranuronic acid / beta-D-galacturonic acid / D-galacturonic acid / galacturonic acid


Type: D-saccharide, beta linking / Mass: 194.139 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C6H10O7 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGalpAbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranuronic acidCOMMON NAMEGMML 1.0
b-D-GalpAIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalASNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1266 / 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: 2.46 Å3/Da / Density % sol: 50.02 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100 mM MOPSO buffer (pH6.5), 12.5% PEG4000, and 20% 1,2,6-hexanetriol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54056 Å
DetectorType: DECTRIS PILATUS3 R 200K-A / Detector: PIXEL / Date: Jan 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2.4→19.95 Å / Num. obs: 107088 / % possible obs: 99.7 % / Redundancy: 5.4 % / CC1/2: 0.972 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.065 / Rrim(I) all: 0.154 / Net I/σ(I): 7.2
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
2.4-2.443.30.4551712852570.8040.2980.546299.8
13.15-19.944.90.06223434770.9940.0280.06812.170.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimless0.7.7data scaling
PDB_EXTRACT3.27data extraction
CrysalisProdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6D1N

6d1n


Resolution: 2.4→19.95 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.875 / SU B: 9.819 / SU ML: 0.216 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.527 / ESU R Free: 0.286 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 5309 5 %RANDOM
Rwork0.1996 ---
obs0.2025 100697 98.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 105.36 Å2 / Biso mean: 21.632 Å2 / Biso min: 2.88 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å20 Å20.24 Å2
2--1.74 Å2-0 Å2
3----1.4 Å2
Refinement stepCycle: final / Resolution: 2.4→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19388 0 56 1266 20710
Biso mean--44.14 21.7 -
Num. residues----2336
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01319944
X-RAY DIFFRACTIONr_bond_other_d0.0010.01518604
X-RAY DIFFRACTIONr_angle_refined_deg1.5291.65427028
X-RAY DIFFRACTIONr_angle_other_deg1.2261.5942808
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.98452320
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43522.5931188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.746153472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.60315136
X-RAY DIFFRACTIONr_chiral_restr0.0690.22508
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0222540
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024884
LS refinement shellResolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 390 -
Rwork0.28 7416 -
all-7806 -
obs--98.91 %

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