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- PDB-9kcz: Crystal structure of Bacteroides ovatus KduI1 responsible for met... -

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Basic information

Entry
Database: PDB / ID: 9kcz
TitleCrystal structure of Bacteroides ovatus KduI1 responsible for metabolism of glycosaminoglycan
Components4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
KeywordsISOMERASE / Glycosaminoglycan metabolism / Bacteroides
Function / homology
Function and homology information


5-dehydro-4-deoxy-D-glucuronate isomerase / 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase activity / D-galacturonate catabolic process / D-glucuronate catabolic process / pectin catabolic process / zinc ion binding
Similarity search - Function
5-keto 4-deoxyuronate isomerase / 5-keto-4-deoxyuronate isomerase, N-terminal / KduI/IolB isomerase / KduI/IolB family / RmlC-like cupin domain superfamily / RmlC-like jelly roll fold
Similarity search - Domain/homology
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
Similarity search - Component
Biological speciesBacteroides ovatus ATCC 8483 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 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 KduI1 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

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Assembly

Deposited unit
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,44114
Polymers196,7046
Non-polymers7378
Water8,107450
1
A: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules

B: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase


Theoretical massNumber of molelcules
Total (without water)65,7524
Polymers65,5682
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2410 Å2
ΔGint-12 kcal/mol
Surface area20360 Å2
MethodPISA
2
C: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
D: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9376
Polymers65,5682
Non-polymers3684
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2900 Å2
ΔGint-10 kcal/mol
Surface area20190 Å2
MethodPISA
3
E: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules

F: 4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7524
Polymers65,5682
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y+1/2,-z1
Buried area2520 Å2
ΔGint-10 kcal/mol
Surface area20140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.121, 99.372, 102.279
Angle α, β, γ (deg.)90.00, 119.72, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
4-deoxy-L-threo-5-hexosulose-uronate ketol-isomerase


Mass: 32784.062 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides ovatus ATCC 8483 (bacteria)
Gene: BACOVA_00140 / Production host: Escherichia coli B (bacteria)
References: UniProt: A0AAN3ACN9, 5-dehydro-4-deoxy-D-glucuronate isomerase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 48.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: PEG 10000, glycerol, TRIS, sodium chloride

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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: 1.89→45.6 Å / Num. obs: 264658 / % possible obs: 94.3 % / Redundancy: 2.91 % / CC1/2: 0.998 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.062 / Net I/av σ(I): 11.75 / Net I/σ(I): 11.75
Reflection shellResolution: 1.89→2 Å / Redundancy: 2.44 % / Rmerge(I) obs: 0.68 / Num. unique obs: 34658 / CC1/2: 0.657 / Rrim(I) all: 0.843 / % possible all: 76.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→45.6 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.952 / SU B: 4.41 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22416 6805 5 %RANDOM
Rwork0.19343 ---
obs0.19495 129290 95.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.176 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0 Å2-0.77 Å2
2--4.06 Å20 Å2
3----1.15 Å2
Refinement stepCycle: 1 / Resolution: 1.89→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12183 0 48 450 12681
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212535
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611530
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.82516959
X-RAY DIFFRACTIONr_angle_other_deg0.4081.75326547
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.74951523
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.162576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.762102047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0540.21795
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0214799
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022949
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_it1.7933.6526128
X-RAY DIFFRACTIONr_mcbond_other1.7933.6526128
X-RAY DIFFRACTIONr_mcangle_it2.756.5497639
X-RAY DIFFRACTIONr_mcangle_other2.756.557640
X-RAY DIFFRACTIONr_scbond_it2.123.866407
X-RAY DIFFRACTIONr_scbond_other2.123.866408
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.4087.0059321
X-RAY DIFFRACTIONr_long_range_B_refined4.94934.6913021
X-RAY DIFFRACTIONr_long_range_B_other4.94734.5512956
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.89→1.938 Å
RfactorNum. reflection% reflection
Rfree0.383 366 -
Rwork0.361 6949 -
obs--69.89 %

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