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- PDB-9kd2: Crystal structure of Bacteroides ovatus DhuD complexed with NAD+ ... -

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Basic information

Entry
Database: PDB / ID: 9kd2
TitleCrystal structure of Bacteroides ovatus DhuD complexed with NAD+ responsible for metabolism of glycosaminoglycan
ComponentsOxidoreductase, short chain dehydrogenase/reductase family protein
KeywordsOXIDOREDUCTASE / Reductase / NAD+ / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Oxidoreductase, short chain dehydrogenase/reductase family protein
Function and homology information
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsTakase, R. / 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 complexed with NAD+ responsible for metabolism of glycosaminoglycan
Authors: Takase, R. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,44212
Polymers177,4626
Non-polymers3,9816
Water362
1
A: Oxidoreductase, short chain dehydrogenase/reductase family protein
B: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4814
Polymers59,1542
Non-polymers1,3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5600 Å2
ΔGint-29 kcal/mol
Surface area21050 Å2
MethodPISA
2
C: Oxidoreductase, short chain dehydrogenase/reductase family protein
D: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4814
Polymers59,1542
Non-polymers1,3272
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5580 Å2
ΔGint-27 kcal/mol
Surface area20840 Å2
MethodPISA
3
E: Oxidoreductase, short chain dehydrogenase/reductase family protein
F: Oxidoreductase, short chain dehydrogenase/reductase family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4814
Polymers59,1542
Non-polymers1,3272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5590 Å2
ΔGint-28 kcal/mol
Surface area20970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.943, 126.911, 71.657
Angle α, β, γ (deg.)90.00, 102.38, 90.00
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 29576.922 Da / Num. of mol.: 6
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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: PEG 8000, 2-propanol, HEPES, 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: Jul 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→48.69 Å / Num. obs: 25615 / % possible obs: 98.9 % / Redundancy: 3.08 % / CC1/2: 0.998 / Rmerge(I) obs: 0.071 / Rrim(I) all: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 3.1→3.28 Å / Redundancy: 3.19 % / Rmerge(I) obs: 0.645 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4095 / CC1/2: 0.812 / Rrim(I) all: 0.774 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→48.69 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.935 / SU B: 31.765 / SU ML: 0.492 / Cross valid method: THROUGHOUT / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24175 1281 5 %RANDOM
Rwork0.19537 ---
obs0.19773 24329 99.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.291 Å2
Baniso -1Baniso -2Baniso -3
1-4.36 Å20 Å2-3.54 Å2
2--4.2 Å2-0 Å2
3----6.38 Å2
Refinement stepCycle: 1 / Resolution: 3.1→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11592 0 264 2 11858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212096
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611543
X-RAY DIFFRACTIONr_angle_refined_deg0.9661.79416431
X-RAY DIFFRACTIONr_angle_other_deg0.3581.73726571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.75351539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.738565
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.247101930
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0450.21869
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214062
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022628
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_it5.15510.1586192
X-RAY DIFFRACTIONr_mcbond_other5.14810.1586192
X-RAY DIFFRACTIONr_mcangle_it8.30918.257719
X-RAY DIFFRACTIONr_mcangle_other8.3118.257720
X-RAY DIFFRACTIONr_scbond_it4.81510.7125904
X-RAY DIFFRACTIONr_scbond_other4.81410.7125905
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other8.0519.6218713
X-RAY DIFFRACTIONr_long_range_B_refined11.58399.413438
X-RAY DIFFRACTIONr_long_range_B_other11.58299.413439
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.1→3.176 Å
RfactorNum. reflection% reflection
Rfree0.371 92 -
Rwork0.388 1751 -
obs--97.05 %

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