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- PDB-6jr8: Flavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A... -

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Basic information

Entry
Database: PDB / ID: 6jr8
TitleFlavobacterium johnsoniae GH31 dextranase, FjDex31A, mutant D412A complexed with isomaltotriose
ComponentsCandidate alpha-glycosidase Glycoside hydrolase family 31
KeywordsHYDROLASE / dextranase / Flavobacterium johnsoniae / dextran / isomaltose / GH31
Function / homology
Function and homology information


: / alpha-glucosidase / carbohydrate binding
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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.country ..._chem_comp.type / _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: Data collection / Database references / Category: chem_comp / citation / citation_author
Item: _chem_comp.type / _citation.journal_volume ..._chem_comp.type / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)388,34425
Polymers384,5544
Non-polymers3,79021
Water65,2323621
1
A: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9385
Polymers96,1381
Non-polymers8004
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area300 Å2
ΔGint-11 kcal/mol
Surface area28730 Å2
MethodPISA
2
B: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1757
Polymers96,1381
Non-polymers1,0366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28750 Å2
MethodPISA
3
C: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,0566
Polymers96,1381
Non-polymers9185
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28810 Å2
MethodPISA
4
D: Candidate alpha-glycosidase Glycoside hydrolase family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,1757
Polymers96,1381
Non-polymers1,0366
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area28630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.370, 112.625, 114.172
Angle α, β, γ (deg.)111.06, 92.98, 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: 96138.469 Da / Num. of mol.: 4 / Mutation: D412A
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: Polysaccharide
alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1a_1-5]/1-1-1/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#3: Chemical
ChemComp-ACT / ACETATE ION


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


Mass: 118.174 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3621 / 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: 2.91 Å3/Da / Density % sol: 57.72 %
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: Dec 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→47.4 Å / Num. obs: 378141 / % possible obs: 96.9 % / Redundancy: 2 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 15.3
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2 / Num. unique obs: 18689 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JR6

6jr6


Resolution: 1.8→47.38 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.093 / 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
Rfree0.1736 19153 5.1 %RANDOM
Rwork0.1499 ---
obs0.1512 358984 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 98.34 Å2 / Biso mean: 20.26 Å2 / Biso min: 9.02 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→47.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26328 0 256 3621 30205
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01327307
X-RAY DIFFRACTIONr_bond_other_d0.0350.01724400
X-RAY DIFFRACTIONr_angle_refined_deg1.781.65336954
X-RAY DIFFRACTIONr_angle_other_deg2.3741.58656842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.67853244
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.22323.5291496
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.016154588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.34615120
X-RAY DIFFRACTIONr_chiral_restr0.1240.23381
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0230516
X-RAY DIFFRACTIONr_gen_planes_other0.0090.025924
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.258 1343 -
Rwork0.254 25533 -
all-26876 -
obs--93.09 %

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