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- PDB-9tk5: Room temperature structure of urocanate reductase in complex with... -

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Basic information

Entry
Database: PDB / ID: 9tk5
TitleRoom temperature structure of urocanate reductase in complex with urocanate in citrate condition
ComponentsUrocanate reductase
KeywordsOXIDOREDUCTASE / urocanate reductase
Function / homology
Function and homology information


urocanate reductase / oxidoreductase activity, acting on the CH-CH group of donors / FMN binding / plasma membrane / cytoplasm
Similarity search - Function
Flavocytochrome c / : / FMN-binding / FMN-binding domain / FMN_bind / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile.
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / PHOSPHATE ION / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID / Urocanate reductase
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAggarwal, S. / Gurav, N. / Oksanen, E. / Lindkvist-Petersson, K. / Venskutonyte, R.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2020-02028 Sweden
Swedish Research Council2024-02673 Sweden
Other privateDIA2020-500
Other privateDIA2022-706
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2026
Title: Structural insights into urocanate reductase using room-temperature X-ray crystallography.
Authors: Aggarwal, S. / Gurav, N. / Oksanen, E. / Lindkvist-Petersson, K. / Venskutonyte, R.
History
DepositionDec 8, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 20, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0265
Polymers49,9851
Non-polymers1,0424
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-31 kcal/mol
Surface area16960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.176, 126.176, 66.729
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Space group name HallP312"
Symmetry operation#1: x,y,z
#2: -y,x-y,z+1/3
#3: -x+y,-x,z+2/3
#4: x-y,-y,-z+2/3
#5: -x,-x+y,-z+1/3
#6: y,x,-z

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Urocanate reductase


Mass: 49984.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shewanella oneidensis MR-1 (bacteria) / Gene: urdA, SO_4620 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CVD0, urocanate reductase

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Non-polymers , 5 types, 284 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-URO / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID


Mass: 138.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.07 Å3/Da / Density % sol: 59.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 20 % PEG 8000, 0.2 M ammonium citrate, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.8→45.84 Å / Num. obs: 56836 / % possible obs: 100 % / Redundancy: 10.2 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.2
Reflection shellResolution: 1.8→1.84 Å / Rmerge(I) obs: 1.116 / Num. unique obs: 3321 / CC1/2: 0.826

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.97 Å / SU ML: 0.2438 / Cross valid method: FREE R-VALUE / σ(F): 1.19 / Phase error: 18.233
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.169 2821 4.97 %
Rwork0.1491 53900 -
obs0.1501 56721 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.97 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 69 280 3804
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00633661
X-RAY DIFFRACTIONf_angle_d0.80024969
X-RAY DIFFRACTIONf_chiral_restr0.0589546
X-RAY DIFFRACTIONf_plane_restr0.0069639
X-RAY DIFFRACTIONf_dihedral_angle_d12.78391374
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.830.51531540.48242623X-RAY DIFFRACTION99.39
1.83-1.860.34281450.33792662X-RAY DIFFRACTION99.75
1.86-1.90.28641400.25812675X-RAY DIFFRACTION99.79
1.9-1.940.25151270.21812692X-RAY DIFFRACTION99.86
1.94-1.980.23691430.19812651X-RAY DIFFRACTION99.75
1.98-2.030.21631350.17332693X-RAY DIFFRACTION99.75
2.03-2.080.18311420.16922671X-RAY DIFFRACTION100
2.08-2.130.21091450.16622685X-RAY DIFFRACTION99.93
2.13-2.20.20341230.17182684X-RAY DIFFRACTION99.82
2.2-2.270.20751870.16272631X-RAY DIFFRACTION99.89
2.27-2.350.18931110.16892726X-RAY DIFFRACTION100
2.35-2.440.1971240.15422683X-RAY DIFFRACTION99.86
2.44-2.550.16951200.15932722X-RAY DIFFRACTION99.96
2.55-2.690.16791400.15732705X-RAY DIFFRACTION99.89
2.69-2.860.18511440.16482698X-RAY DIFFRACTION100
2.86-3.080.17961480.14712695X-RAY DIFFRACTION99.96
3.08-3.390.13641370.1382718X-RAY DIFFRACTION99.96
3.39-3.880.16031380.11622739X-RAY DIFFRACTION100
3.88-4.880.11561610.09812722X-RAY DIFFRACTION99.97
4.88-31.970.12281570.12372825X-RAY DIFFRACTION99.47

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