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- PDB-6t85: Urocanate reductase in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 6t85
TitleUrocanate reductase in complex with ADP
ComponentsUrocanate reductase
KeywordsOXIDOREDUCTASE / urocanate reductase / bacterial enzyme
Function / homology
Function and homology information


urocanate reductase / FMN binding / oxidoreductase activity / plasma membrane / cytoplasm
Similarity search - Function
Flavocytochrome c / : / FMN-binding / FMN-binding domain / FMN_bind / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain superfamily / FAD-dependent oxidoreductase 2, FAD binding domain / FAD binding domain ...Flavocytochrome c / : / FMN-binding / FMN-binding domain / FMN_bind / Flavocytochrome C3; Chain A, domain 1 / Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain / 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. / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Urocanate reductase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.1 Å
AuthorsVenskutonyte, R. / Lindkvist-Petersson, K.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-01319 Sweden
Swedish Research Council2017-05816 Sweden
European Research Council780659 Sweden
CitationJournal: Nat Commun / Year: 2021
Title: Structural characterization of the microbial enzyme urocanate reductase mediating imidazole propionate production.
Authors: Venskutonyte, R. / Koh, A. / Stenstrom, O. / Khan, M.T. / Lundqvist, A. / Akke, M. / Backhed, F. / Lindkvist-Petersson, K.
History
DepositionOct 24, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,86510
Polymers49,9851
Non-polymers8819
Water13,926773
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-58 kcal/mol
Surface area17450 Å2
Unit cell
Length a, b, c (Å)41.839, 95.762, 63.200
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Urocanate reductase


Mass: 49984.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Truncated UrdA, construct comprising residues 130-582 and a C-terminal 6xHis tag.
Source: (gene. exp.) Shewanella oneidensis (strain MR-1) (bacteria)
Strain: MR-1 / Gene: urdA, SO_4620 / Plasmid: pET-24a(+) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CVD0, urocanate reductase
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.43 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20 % PEG4000 0.1 M MgCl2 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: P13 (MX1) / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.1→63.19 Å / Num. obs: 198264 / % possible obs: 98.6 % / Redundancy: 8.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.036 / Rrim(I) all: 0.111 / Net I/σ(I): 9.5 / Num. measured all: 1753417 / Scaling rejects: 452
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.1-1.123.20.8272931891490.5430.5380.9911.292.4
6.02-63.1910.70.0611356912740.9950.020.06433.3100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.14-3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4C

1d4c


Resolution: 1.1→63.189 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 12.1
RfactorNum. reflection% reflection
Rfree0.1297 9770 4.93 %
Rwork0.1075 --
obs0.1086 198098 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 60.89 Å2 / Biso mean: 14.9925 Å2 / Biso min: 5.76 Å2
Refinement stepCycle: final / Resolution: 1.1→63.189 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3505 0 86 826 4417
Biso mean--15.74 28.56 -
Num. residues----459

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