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- PDB-8q9v: S-methylthiourocanate hydratase from Variovorax sp. RA8 in comple... -

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Basic information

Entry
Database: PDB / ID: 8q9v
TitleS-methylthiourocanate hydratase from Variovorax sp. RA8 in complex with NAD+ and imidazolone propionate
Componentsurocanate hydratase
KeywordsOXIDOREDUCTASE / S-methylergothioneine S-methylthiourocanate NAD+
Function / homology
Function and homology information


urocanate hydratase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate / Lyases; Carbon-oxygen lyases; Hydro-lyases / nucleotide binding
Similarity search - Function
Urocanase conserved site / Urocanase signature. / Urocanase / Urocanase, Rossmann-like domain / Urocanase, N-terminal domain / Urocanase, C-terminal domain / Urocanase superfamily / Urocanase, central domain superfamily / Urocanase Rossmann-like domain / Urocanase N-terminal domain / Urocanase C-terminal domain
Similarity search - Domain/homology
ACETIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / : / S-methyl thiourocanate hydratase
Similarity search - Component
Biological speciesVariovorax sp. RA8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsVasseur, C.M. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation182023 Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2024
Title: Structure and Substrate Specificity of S -Methyl Thiourocanate Hydratase.
Authors: Vasseur, C.M. / Karunasegaram, D. / Seebeck, F.P.
History
DepositionAug 21, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7526
Polymers58,6171
Non-polymers1,1365
Water7,206400
1
A: urocanate hydratase
hetero molecules

A: urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,50512
Polymers117,2332
Non-polymers2,27210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area8990 Å2
ΔGint-60 kcal/mol
Surface area33560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.511, 96.511, 147.585
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212
Components on special symmetry positions
IDModelComponents
11A-1224-

HOH

21A-1285-

HOH

31A-1287-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein urocanate hydratase


Mass: 58616.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Variovorax sp. RA8 (bacteria) / Gene: hutU_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P2DXK2

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Non-polymers , 6 types, 405 molecules

#2: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#3: Chemical ChemComp-O66 / 3-[(4~{R})-5-oxidanylidene-1,4-dihydroimidazol-4-yl]propanoic acid / Imidazol-4-one-5-propionic acid


Mass: 156.139 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#5: Chemical ChemComp-ACY / ACETIC ACID


Mass: 60.052 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.38 Å3/Da / Density % sol: 63.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 %w/v PEG 3350 0.2 M Na3 Cit 0.1 M BIS-TRIS prop 7.5 pH

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→49.2 Å / Num. obs: 80319 / % possible obs: 99.97 % / Redundancy: 1 % / CC1/2: 0.996 / Net I/σ(I): 8.89
Reflection shellResolution: 2.2→2.279 Å / Mean I/σ(I) obs: 1.58 / Num. unique obs: 7880 / CC1/2: 0.628

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Processing

Software
NameVersionClassification
PHENIX(1.17.1_3660: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→49.2 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.207 3823 4.9 %
Rwork0.1615 --
obs0.1637 78036 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→49.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4066 0 76 400 4542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0144218
X-RAY DIFFRACTIONf_angle_d1.735719
X-RAY DIFFRACTIONf_dihedral_angle_d15.666650
X-RAY DIFFRACTIONf_chiral_restr0.071640
X-RAY DIFFRACTIONf_plane_restr0.008773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.30281510.28412690X-RAY DIFFRACTION100
2.23-2.260.30561530.27352753X-RAY DIFFRACTION100
2.26-2.290.27431400.27652759X-RAY DIFFRACTION100
2.29-2.320.31081580.272772X-RAY DIFFRACTION100
2.32-2.360.26411020.25652795X-RAY DIFFRACTION100
2.36-2.390.30711380.25452692X-RAY DIFFRACTION100
2.39-2.430.31371550.23732727X-RAY DIFFRACTION100
2.43-2.470.24731440.23612803X-RAY DIFFRACTION100
2.47-2.520.25281440.21632709X-RAY DIFFRACTION100
2.52-2.570.25861680.21912715X-RAY DIFFRACTION100
2.57-2.620.23981620.20022755X-RAY DIFFRACTION100
2.62-2.680.25831320.19662736X-RAY DIFFRACTION100
2.68-2.740.24331120.1872774X-RAY DIFFRACTION100
2.74-2.810.20721260.18232772X-RAY DIFFRACTION100
2.81-2.880.25341580.18012705X-RAY DIFFRACTION100
2.88-2.970.21461560.16642737X-RAY DIFFRACTION100
2.97-3.060.26451420.16862743X-RAY DIFFRACTION100
3.06-3.170.2331250.16892784X-RAY DIFFRACTION100
3.17-3.30.20881680.16142722X-RAY DIFFRACTION100
3.3-3.450.17481280.15032810X-RAY DIFFRACTION100
3.45-3.630.19321260.13442723X-RAY DIFFRACTION100
3.63-3.860.1651200.11592791X-RAY DIFFRACTION100
3.86-4.160.1141940.10892786X-RAY DIFFRACTION100
4.16-4.580.14951620.10042724X-RAY DIFFRACTION100
4.58-5.240.16651240.1132783X-RAY DIFFRACTION100
5.24-6.590.16891580.13882720X-RAY DIFFRACTION100
6.6-49.20.16061770.12412733X-RAY DIFFRACTION100

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