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- PDB-6jr6: Flavobacterium johnsoniae GH31 dextranase, FjDex31A -

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Basic information

Entry
Database: PDB / ID: 6jr6
TitleFlavobacterium johnsoniae GH31 dextranase, FjDex31A
ComponentsCandidate alpha-glycosidase Glycoside hydrolase family 31
KeywordsHYDROLASE / dextranase / Flavobacterium johnsoniae / dextran / isomaltose / GH31
Function / homology
Function and homology information


alpha-1,4-glucosidase activity / alpha-glucosidase / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily ...: / Domain of unknown function DUF5110 / Domain of unknown function (DUF5110) / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
ACETATE ION / Candidate alpha-glycosidase Glycoside hydrolase family 31
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å
AuthorsTonozuka, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science16K07687 Japan
CitationJournal: Febs J. / Year: 2020
Title: Structural insights into polysaccharide recognition by Flavobacterium johnsoniae dextranase, a member of glycoside hydrolase family 31.
Authors: Tsutsumi, K. / Gozu, Y. / Nishikawa, A. / Tonozuka, T.
History
DepositionApr 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Apr 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 1.3Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Candidate alpha-glycosidase Glycoside hydrolase family 31
B: Candidate alpha-glycosidase Glycoside hydrolase family 31
C: Candidate alpha-glycosidase Glycoside hydrolase family 31
D: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)385,91116
Polymers384,7304
Non-polymers1,18212
Water42,8942381
1
A: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4784
Polymers96,1821
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28780 Å2
MethodPISA
2
B: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4784
Polymers96,1821
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28970 Å2
MethodPISA
3
C: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4784
Polymers96,1821
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28790 Å2
MethodPISA
4
D: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4784
Polymers96,1821
Non-polymers2953
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-10 kcal/mol
Surface area28960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.471, 112.739, 114.250
Angle α, β, γ (deg.)111.13, 92.86, 114.54
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Candidate alpha-glycosidase Glycoside hydrolase family 31 / Dextranase


Mass: 96182.477 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / UW101 / Gene: Fjoh_4430 / Production host: Escherichia coli (E. coli) / References: UniProt: A5FBI1, alpha-glucosidase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2381 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.92 Å3/Da / Density % sol: 57.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 100 mM sodium acetate buffer, 8% (w/v) polyethylene glycol 20000, and 8% 2-methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48.5 Å / Num. obs: 275382 / % possible obs: 97.1 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.8
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.334 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 13574 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2→48.45 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.164 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: Leu308-Gln309 adopts a cis conformation yet the electron density is clearly seen HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1993 12837 5 %RANDOM
Rwork0.1646 ---
obs0.1664 244228 90.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 100.4 Å2 / Biso mean: 28.199 Å2 / Biso min: 14.55 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2→48.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26340 0 80 2381 28801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01327140
X-RAY DIFFRACTIONr_bond_other_d0.0350.01724240
X-RAY DIFFRACTIONr_angle_refined_deg1.7381.64636732
X-RAY DIFFRACTIONr_angle_other_deg2.3061.5856464
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.69253244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.09523.5471500
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.627154592
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3515120
X-RAY DIFFRACTIONr_chiral_restr0.1180.23324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0230532
X-RAY DIFFRACTIONr_gen_planes_other0.0070.025924
LS refinement shellResolution: 2.001→2.053 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.265 576 -
Rwork0.238 11310 -
all-11886 -
obs--56.45 %

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