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- PDB-6t86: Urocanate reductase in complex with FAD -

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Basic information

Entry
Database: PDB / ID: 6t86
TitleUrocanate reductase in complex with FAD
ComponentsUrocanate reductase
KeywordsOXIDOREDUCTASE / urocanate reductase / bacterial enzyme
Function / homology
Function and homology information


urocanate reductase / steroid metabolic process / FMN binding / oxidoreductase activity / plasma membrane
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 / Urocanate reductase
Similarity search - Component
Biological speciesShewanella oneidensis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.56 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

Downloads & links

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Assembly

Deposited unit
A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,75215
Polymers49,9851
Non-polymers1,76814
Water3,423190
1
A: Urocanate reductase
hetero molecules

A: Urocanate reductase
hetero molecules

A: Urocanate reductase
hetero molecules

A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,00860
Polymers199,9384
Non-polymers7,07056
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_655-x+1,-y,z1
crystal symmetry operation8_556x-y,-y,-z+11
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area20950 Å2
ΔGint-520 kcal/mol
Surface area64860 Å2
MethodPISA
2
A: Urocanate reductase
hetero molecules

A: Urocanate reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,50430
Polymers99,9692
Non-polymers3,53528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_556x,x-y,-z+11
Buried area10320 Å2
ΔGint-276 kcal/mol
Surface area32590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.786, 159.786, 75.491
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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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
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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8CVD0, urocanate reductase

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Non-polymers , 6 types, 204 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.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#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.: 190 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH 8.5 2 M (NH4)2SO4 5% xylitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.56→46.13 Å / Num. obs: 18422 / % possible obs: 98.1 % / Redundancy: 18.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.175 / Rpim(I) all: 0.038 / Rrim(I) all: 0.179 / Net I/σ(I): 15.3 / Num. measured all: 346148 / Scaling rejects: 1173
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
2.56-2.676.20.651220619730.8640.2740.712.689.1
8.87-46.1320.90.094112265370.9980.020.09627.399.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.7.4data scaling
PHASERphasing
PHENIX1.15.2-3472refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1D4C

1d4c


Resolution: 2.56→46.126 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 23.3
RfactorNum. reflection% reflection
Rfree0.2316 916 5.01 %
Rwork0.1747 --
obs0.1775 18292 97.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 115.43 Å2 / Biso mean: 32.73 Å2 / Biso min: 14.42 Å2
Refinement stepCycle: final / Resolution: 2.56→46.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 105 190 3750
Biso mean--45.73 33.54 -
Num. residues----454
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.39020.99680.86023.6506-0.39623.2159-0.02110.44090.2059-0.0648-0.03260.0671-0.3746-0.25520.05890.23870.0588-0.01540.22270.0030.156241.219621.657510.1548
22.5461-0.18810.45431.50930.24820.60040.02570.12640.098-0.0098-0.0298-0.1828-0.07490.13440.00210.2044-0.0060.01490.2104-0.02930.173559.97416.017917.797
33.49521.83021.32755.83990.67924.03050.1256-0.17070.12780.0257-0.28190.4923-0.0162-0.37410.1640.14850.0057-0.00530.304-0.02230.24532.27520.443514.5334
42.06261.2979-0.2342.1928-2.3599.09110.1639-0.43250.07280.1566-0.04950.12480.395-0.008-0.13090.25830.00570.05170.2656-0.02110.345643.066913.748238.1021
52.9227-0.33412.01780.75850.05692.377-0.0029-0.0163-0.1345-0.01630.04140.09010.0464-0.0339-0.04150.2193-0.00480.04890.2020.00930.218451.106215.318834.866
63.43131.2494-0.89765.0199-1.09772.10060.02950.0849-0.15890.0032-0.03270.1242-0.0431-0.0039-0.01980.16230.0372-0.02810.1964-0.03320.1564.125719.153246.2596
75.9929-2.5521-0.31484.3828-0.98191.8335-0.2491-0.6586-0.09960.51740.238-0.014-0.09170.07410.01130.236-0.0257-0.01590.25280.00140.182769.757620.153857.3766
82.3150.43391.8990.19360.7523.11080.09490.0018-0.23040.01610.0034-0.06560.13070.0523-0.10590.2618-0.0040.01540.14810.04660.279657.779810.526935.5552
92.6843-0.493-0.08631.4694-0.68540.3594-0.03360.0501-0.1179-0.11630.0266-0.03740.2567-0.0729-0.00340.276-0.02340.00210.1459-0.01580.247649.867910.435918.3099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 129 through 154 )A129 - 154
2X-RAY DIFFRACTION2chain 'A' and (resid 155 through 275 )A155 - 275
3X-RAY DIFFRACTION3chain 'A' and (resid 276 through 318 )A276 - 318
4X-RAY DIFFRACTION4chain 'A' and (resid 319 through 343 )A319 - 343
5X-RAY DIFFRACTION5chain 'A' and (resid 344 through 397 )A344 - 397
6X-RAY DIFFRACTION6chain 'A' and (resid 398 through 453 )A398 - 453
7X-RAY DIFFRACTION7chain 'A' and (resid 454 through 490 )A454 - 490
8X-RAY DIFFRACTION8chain 'A' and (resid 491 through 542 )A491 - 542
9X-RAY DIFFRACTION9chain 'A' and (resid 543 through 582 )A543 - 582

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