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- PDB-9tk7: Cryogenic temperature structure of urocanate reductase in complex... -

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Basic information

Entry
Database: PDB / ID: 9tk7
TitleCryogenic temperature structure of urocanate reductase in complex with imidazole propionate and sulfate
ComponentsUrocanate reductase
KeywordsOXIDOREDUCTASE / urocanate reductase / imidazole propionate
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 / 3-(1~{H}-imidazol-5-yl)propanoic acid / Urocanate reductase
Similarity search - Component
Biological speciesShewanella oneidensis MR-1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)51,77013
Polymers49,9851
Non-polymers1,78512
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3280 Å2
ΔGint-59 kcal/mol
Surface area17450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.143, 124.143, 66.279
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 , 6 types, 544 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-MWQ / 3-(1~{H}-imidazol-5-yl)propanoic acid


Mass: 140.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.95 Å3/Da / Density % sol: 58.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20 % PEG 8000, 0.2 M (NH4)2SO4 and 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9794 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.5→66.28 Å / Num. obs: 93985 / % possible obs: 100 % / Redundancy: 20 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.081 / Net I/σ(I): 21.9
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 4591 / CC1/2: 0.772

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→53.76 Å / SU ML: 0.1156 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 12.8615
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1392 4703 5.01 %
Rwork0.1129 89231 -
obs0.1142 93934 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.68 Å2
Refinement stepCycle: LAST / Resolution: 1.5→53.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 116 532 4103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00923711
X-RAY DIFFRACTIONf_angle_d1.055032
X-RAY DIFFRACTIONf_chiral_restr0.0616550
X-RAY DIFFRACTIONf_plane_restr0.0106639
X-RAY DIFFRACTIONf_dihedral_angle_d13.18071397
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.520.22651710.17712907X-RAY DIFFRACTION100
1.52-1.530.2231370.17472968X-RAY DIFFRACTION99.94
1.53-1.550.20441720.15732931X-RAY DIFFRACTION100
1.55-1.570.21561780.15052956X-RAY DIFFRACTION100
1.57-1.590.19341690.1462934X-RAY DIFFRACTION99.97
1.59-1.620.17491340.13092985X-RAY DIFFRACTION100
1.62-1.640.18781260.12582949X-RAY DIFFRACTION99.94
1.64-1.660.18391680.11572951X-RAY DIFFRACTION99.97
1.66-1.690.1691550.10812930X-RAY DIFFRACTION100
1.69-1.720.16071560.10422981X-RAY DIFFRACTION99.97
1.72-1.750.16211720.09952973X-RAY DIFFRACTION99.97
1.75-1.780.15331580.0982932X-RAY DIFFRACTION100
1.78-1.810.12591800.09642903X-RAY DIFFRACTION100
1.81-1.850.13681680.08912979X-RAY DIFFRACTION100
1.85-1.890.14791380.0912996X-RAY DIFFRACTION100
1.89-1.930.12051560.09232941X-RAY DIFFRACTION100
1.93-1.980.12691670.08872949X-RAY DIFFRACTION100
1.98-2.040.1191890.0842957X-RAY DIFFRACTION100
2.04-2.10.13261540.08622952X-RAY DIFFRACTION99.97
2.1-2.160.12061310.08893005X-RAY DIFFRACTION100
2.16-2.240.13541580.08892964X-RAY DIFFRACTION100
2.24-2.330.13391370.09152996X-RAY DIFFRACTION99.97
2.33-2.440.12731440.09032991X-RAY DIFFRACTION100
2.44-2.560.1171650.10522983X-RAY DIFFRACTION100
2.57-2.730.1481570.10852982X-RAY DIFFRACTION100
2.73-2.940.13511520.1183020X-RAY DIFFRACTION100
2.94-3.230.15061910.12112942X-RAY DIFFRACTION99.94
3.23-3.70.13271220.11613078X-RAY DIFFRACTION100
3.7-4.660.1051680.10943034X-RAY DIFFRACTION100
4.66-53.760.16121300.15593162X-RAY DIFFRACTION99.58

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