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- PDB-9kd1: Crystal structure of Bacteroides ovatus DhuD responsible for meta... -

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Basic information

Entry
Database: PDB / ID: 9kd1
TitleCrystal structure of Bacteroides ovatus DhuD responsible for metabolism of glycosaminoglycan
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / Reductase / Glycosaminoglycan metabolism / Bacteroides
Function / homologyShort-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily / ACETATE ION / Oxidoreductase, short chain dehydrogenase/reductase family protein
Function and homology information
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsTakase, R. / Kouda, Y. / Mikami, B. / Hashimoto, W.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)15H04629 Japan
Japan Society for the Promotion of Science (JSPS)18H02166 Japan
Japan Society for the Promotion of Science (JSPS)21H02156 Japan
Yakult Bio-science Foundation Japan
Japan Foundation for Applied Enzymology Japan
Japan Environ and Organic-farming Foundation Japan
CitationJournal: To Be Published
Title: Crystal structure of Bacteroides ovatus DhuD responsible for metabolism of glycosaminoglycan
Authors: Takase, R. / Kouda, Y. / Mikami, B. / Hashimoto, W.
History
DepositionNov 2, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
E: Oxidoreductase, short chain dehydrogenase/reductase family protein
F: Oxidoreductase, short chain dehydrogenase/reductase family protein
G: Oxidoreductase, short chain dehydrogenase/reductase family protein
H: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)236,85212
Polymers236,6158
Non-polymers2364
Water13,763764
1
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
F: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2133
Polymers59,1542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-20 kcal/mol
Surface area21960 Å2
MethodPISA
2
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
E: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2724
Polymers59,1542
Non-polymers1182
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-19 kcal/mol
Surface area22600 Å2
MethodPISA
3
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
H: Oxidoreductase, short chain dehydrogenase/reductase family protein


Theoretical massNumber of molelcules
Total (without water)59,1542
Polymers59,1542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3460 Å2
ΔGint-19 kcal/mol
Surface area22030 Å2
MethodPISA
4
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
G: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2133
Polymers59,1542
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-18 kcal/mol
Surface area22500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.640, 75.446, 102.068
Angle α, β, γ (deg.)97.69, 96.42, 95.33
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Oxidoreductase, short chain dehydrogenase/reductase family protein


Mass: 29576.922 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_00141 / Production host: Escherichia coli B (bacteria) / References: UniProt: A0AAN3ACT3
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG 400, magnesium acetate tetrahydrate, sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Feb 12, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.09→40.99 Å / Num. obs: 120519 / % possible obs: 96.72 % / Redundancy: 3 % / CC1/2: 0.967 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.121 / Net I/σ(I): 14.23
Reflection shellResolution: 2.1→2.14 Å / Rmerge(I) obs: 0.254 / Mean I/σ(I) obs: 3.55 / Num. unique obs: 5925 / CC1/2: 0.921 / Rrim(I) all: 0.309 / % possible all: 85.72

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.09→40.99 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.862 / SU B: 5.498 / SU ML: 0.15 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25192 5884 4.9 %RANDOM
Rwork0.20782 ---
obs0.20997 114634 96.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.723 Å2
Baniso -1Baniso -2Baniso -3
1--1.45 Å2-0.5 Å20.23 Å2
2--1.44 Å2-1.32 Å2
3---0.41 Å2
Refinement stepCycle: 1 / Resolution: 2.09→40.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15577 0 16 764 16357
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.01215875
X-RAY DIFFRACTIONr_bond_other_d0.0010.01615330
X-RAY DIFFRACTIONr_angle_refined_deg1.1461.79121494
X-RAY DIFFRACTIONr_angle_other_deg0.4261.73835253
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42852071
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.544577
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.283102598
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.22427
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218747
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023477
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_it0.9221.8778330
X-RAY DIFFRACTIONr_mcbond_other0.9221.8778330
X-RAY DIFFRACTIONr_mcangle_it1.5283.36610383
X-RAY DIFFRACTIONr_mcangle_other1.5283.36610384
X-RAY DIFFRACTIONr_scbond_it1.1432.0677545
X-RAY DIFFRACTIONr_scbond_other1.1432.0677546
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.923.75311112
X-RAY DIFFRACTIONr_long_range_B_refined3.13317.917668
X-RAY DIFFRACTIONr_long_range_B_other3.08217.7517570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.09→2.14 Å
RfactorNum. reflection% reflection
Rfree0.265 417 -
Rwork0.215 7456 -
obs--85.72 %

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