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- PDB-8wg2: Crystal structure of GH97 glucodextranase mutant E509Q from Flavo... -

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Basic information

Entry
Database: PDB / ID: 8wg2
TitleCrystal structure of GH97 glucodextranase mutant E509Q from Flavobacterium johnsoniae in complex with isomaltotriose
ComponentsCandidate alpha-glucosidase Glycoside hydrolase family 97
KeywordsHYDROLASE / GLYCOSIDE HYDROLASE / GH97 / DEXTRAN / TIM-BARREL / ISOMALTOSE / NIGEROSE
Function / homology
Function and homology information


carbohydrate binding / hydrolase activity / metal ion binding
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / : / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Glycoside hydrolase-type carbohydrate-binding / Aldolase-type TIM barrel / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Candidate alpha-glucosidase Glycoside hydrolase family 97
Similarity search - Component
Biological speciesFlavobacterium johnsoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsKurata, R. / Nakamura, S. / Miyazaki, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K05039 Japan
Japan Society for the Promotion of Science (JSPS)19K15748 Japan
CitationJournal: Febs J. / Year: 2024
Title: Structural insights into alpha-(1→6)-linkage preference of GH97 glucodextranase from Flavobacterium johnsoniae.
Authors: Nakamura, S. / Kurata, R. / Miyazaki, T.
History
DepositionSep 20, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Candidate alpha-glucosidase Glycoside hydrolase family 97
B: Candidate alpha-glucosidase Glycoside hydrolase family 97
C: Candidate alpha-glucosidase Glycoside hydrolase family 97
D: Candidate alpha-glucosidase Glycoside hydrolase family 97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,25712
Polymers311,0794
Non-polymers2,1788
Water8,503472
1
A: Candidate alpha-glucosidase Glycoside hydrolase family 97
B: Candidate alpha-glucosidase Glycoside hydrolase family 97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,6296
Polymers155,5402
Non-polymers1,0894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Candidate alpha-glucosidase Glycoside hydrolase family 97
D: Candidate alpha-glucosidase Glycoside hydrolase family 97
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,6296
Polymers155,5402
Non-polymers1,0894
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)308.210, 103.620, 95.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
Candidate alpha-glucosidase Glycoside hydrolase family 97


Mass: 77769.805 Da / Num. of mol.: 4 / Mutation: E509Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Flavobacterium johnsoniae (strain ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101) (bacteria)
Strain: ATCC 17061 / DSM 2064 / JCM 8514 / NBRC 14942 / NCIMB 11054 / UW101
Gene: Fjoh_4429 / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A5FBI0, glucan 1,6-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.: 2
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: Polysaccharide alpha-D-glucopyranose-(1-6)-alpha-D-glucopyranose-(1-6)-beta-D-glucopyranose


Type: oligosaccharide / Mass: 504.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpa1-6DGlcpa1-6DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5][a2122h-1a_1-5]/1-2-2/a6-b1_b6-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(6+1)][a-D-Glcp]{[(6+1)][a-D-Glcp]{}}}LINUCSPDB-CARE
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / 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: 2.37 Å3/Da / Density % sol: 48.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 12% PEG20000, 200 mM sodium cacodylate buffer (pH 6.0), 200 mM magnesium acetate, 10 mM glucose

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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: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→49.16 Å / Num. obs: 113578 / % possible obs: 100 % / Redundancy: 13 % / CC1/2: 0.996 / Rmerge(I) obs: 0.195 / Rpim(I) all: 0.081 / Rrim(I) all: 0.212 / Net I/σ(I): 12.9
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 12.5 % / Rmerge(I) obs: 1.302 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 69191 / CC1/2: 0.783 / Rpim(I) all: 0.556 / Rrim(I) all: 1.417 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→49.16 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.919 / SU B: 19.536 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R: 0.518 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23398 5817 5.1 %RANDOM
Rwork0.18491 ---
obs0.18743 107681 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.955 Å2
Baniso -1Baniso -2Baniso -3
1--1.56 Å2-0 Å20 Å2
2--0.76 Å2-0 Å2
3---0.79 Å2
Refinement stepCycle: 1 / Resolution: 2.45→49.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21858 0 140 472 22470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01222576
X-RAY DIFFRACTIONr_bond_other_d0.0010.01620484
X-RAY DIFFRACTIONr_angle_refined_deg2.3421.81930631
X-RAY DIFFRACTIONr_angle_other_deg0.7861.77147240
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.61152717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.585592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.779103707
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1070.23253
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0226651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025417
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3821.70810886
X-RAY DIFFRACTIONr_mcbond_other2.3821.70810886
X-RAY DIFFRACTIONr_mcangle_it3.5383.06413597
X-RAY DIFFRACTIONr_mcangle_other3.5383.06413598
X-RAY DIFFRACTIONr_scbond_it3.1731.9211690
X-RAY DIFFRACTIONr_scbond_other3.1731.9211691
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7253.40717035
X-RAY DIFFRACTIONr_long_range_B_refined5.77516.4324708
X-RAY DIFFRACTIONr_long_range_B_other5.77316.4224658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.513 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 463 -
Rwork0.263 7810 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.52630.4847-0.01880.79120.17350.8436-0.06560.16920.0573-0.01820.0607-0.01290.07080.04510.00490.01550.0172-0.02220.1562-0.01760.091289.08424.29327.692
21.930.2043-0.25060.4975-0.14730.96110.116-0.16750.54980.09260.00250.17950.0305-0.0606-0.11850.0294-0.03470.06830.1484-0.10910.385143.5929.04250.154
31.21060.2179-0.01650.8277-0.24760.9644-0.08190.12460.2475-0.25750.11370.2135-0.0188-0.1044-0.03170.1122-0.028-0.11090.13570.03350.1784-8.133-26.315-1.178
41.09850.06580.26270.63550.051.0315-0.0609-0.01520.15130.0217-0.074-0.0698-0.09850.17820.13490.0472-0.0536-0.03330.18560.01560.112937.546-20.53120.544
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 701
2X-RAY DIFFRACTION2B20 - 700
3X-RAY DIFFRACTION3C20 - 703
4X-RAY DIFFRACTION4D20 - 700
5X-RAY DIFFRACTION1A800
6X-RAY DIFFRACTION2B800
7X-RAY DIFFRACTION3C800
8X-RAY DIFFRACTION4D800
9X-RAY DIFFRACTION1E1 - 3
10X-RAY DIFFRACTION2F1 - 3
11X-RAY DIFFRACTION3G1 - 3
12X-RAY DIFFRACTION4H1 - 3

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