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- PDB-9u42: Crystal Structure of Homogentisate 1,2-Dioxygenase from Acinetoba... -

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Basic information

Entry
Database: PDB / ID: 9u42
TitleCrystal Structure of Homogentisate 1,2-Dioxygenase from Acinetobacter in Complex with Zn ion
ComponentsGlyoxalase
KeywordsOXIDOREDUCTASE / Dioxygenase / Aromatic compound metabolism
Function / homology: / Glyoxalase/fosfomycin resistance/dioxygenase domain / Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily / Vicinal oxygen chelate (VOC) domain / Vicinal oxygen chelate (VOC) domain profile. / Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase / Glyoxalase
Function and homology information
Biological speciesAcinetobacter (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsSeo, P.-W. / Hwangbo, S.-A. / Park, S.-Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2023-00219517 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2024-00440289 Korea, Republic Of
CitationJournal: Proteins / Year: 2025
Title: Structural Mimicry Without Glyoxalase I Functional Convergence: A Homogentisate 1,2-Dioxygenase From Acinetobacter.
Authors: Seo, P.W. / Hwangbo, S.A. / Kim, J.S. / Park, S.Y.
History
DepositionMar 19, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 23, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glyoxalase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4173
Polymers21,2291
Non-polymers1882
Water2,972165
1
A: Glyoxalase
hetero molecules

A: Glyoxalase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, Biological unit is a homodimer, although observed as a monomer in gel filtration analysis. Crystallographic packing reveals a homodimeric interface consistent with the biological assembly.
  • 42.8 kDa, 2 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)42,8336
Polymers42,4582
Non-polymers3754
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_454-x-1,y,-z-1/21
Buried area8040 Å2
ΔGint-104 kcal/mol
Surface area16530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.058, 121.250, 54.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-304-

HOH

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Components

#1: Protein Glyoxalase


Mass: 21229.111 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter (bacteria) / Gene: DH17_10945 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0B2UB00
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 165 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Bis-Tris (pH 6.5), 0.05 M Calcium chloride and 30 % (v/v) PEG 550 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→25 Å / Num. obs: 25748 / % possible obs: 98.1 % / Redundancy: 6.8 % / Rpim(I) all: 0.033 / Rrim(I) all: 0.089 / Net I/σ(I): 7.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
1.55-1.585.50.67912360.7530.9270.3070.7480.43796.4
1.58-1.615.90.61312570.8230.950.2690.6710.46196.6
1.61-1.646.50.58112500.8840.9690.240.630.46597.2
1.64-1.676.70.51412600.9060.9750.2090.5560.49596.8
1.67-1.716.80.43412630.9290.9810.1750.4680.53696.6
1.71-1.756.70.36612410.9450.9860.1490.3950.53697.2
1.75-1.796.80.32612660.9610.990.1330.3530.60897.3
1.79-1.846.80.25512610.9730.9930.1030.2750.66997.1
1.84-1.896.70.2212710.9790.9950.090.2380.7698.2
1.89-1.956.30.18413020.9780.9940.0780.2010.97998.3
1.95-2.026.40.14912680.9880.9970.0630.1621.06998.7
2.02-2.17.40.13212790.9880.9970.0520.1421.00998.2
2.1-2.27.40.11412900.9910.9980.0450.1230.99398.6
2.2-2.317.40.10612910.9930.9980.0410.1141.09698.1
2.31-2.467.30.09512990.9950.9990.0370.1021.05299.2
2.46-2.6570.09113140.9940.9990.0360.0980.99699.2
2.65-2.926.30.08113060.9950.9990.0340.0881.05599.2
2.92-3.347.40.06913300.9960.9990.0270.0751.06999.1
3.34-4.27.30.05513430.9980.9990.0220.061.08799.8
4.2-256.60.05714210.9970.9990.0230.0621.03299.5

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→24.8 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1909 1016 4 %
Rwork0.1687 --
obs0.1695 25393 98.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→24.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1382 0 9 165 1556
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111426
X-RAY DIFFRACTIONf_angle_d1.3571926
X-RAY DIFFRACTIONf_dihedral_angle_d21.503526
X-RAY DIFFRACTIONf_chiral_restr0.082202
X-RAY DIFFRACTIONf_plane_restr0.008248
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.630.221400.21953374X-RAY DIFFRACTION97
1.63-1.730.20811420.19313399X-RAY DIFFRACTION97
1.73-1.870.19541420.17873431X-RAY DIFFRACTION98
1.87-2.060.19411440.17183447X-RAY DIFFRACTION98
2.06-2.350.20011460.16563491X-RAY DIFFRACTION99
2.35-2.960.22621480.17823540X-RAY DIFFRACTION99
2.96-24.80.16551540.15533695X-RAY DIFFRACTION100

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