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- PDB-8q9u: S-methylthiourocanate hydratase, variant R450A, from Variovorax s... -

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Basic information

Entry
Database: PDB / ID: 8q9u
TitleS-methylthiourocanate hydratase, variant R450A, from Variovorax sp. RA8 in complex with NAD+
Componentsurocanate hydratase
KeywordsLYASE / urocanase S-methylergothioneine NAD+
Function / homology
Function and homology information


urocanate hydratase / urocanate hydratase activity / L-histidine catabolic process to glutamate and formamide / L-histidine catabolic process to glutamate and formate
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / urocanate hydratase
Similarity search - Component
Biological speciesVariovorax sp. RA8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 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

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Assembly

Deposited unit
A: urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1942
Polymers58,5301
Non-polymers6631
Water2,720151
1
A: urocanate hydratase
hetero molecules

A: urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3884
Polymers117,0612
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,x-y-1,-z1
Buried area8410 Å2
ΔGint-62 kcal/mol
Surface area33710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.947, 95.947, 147.818
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number153
Space group name H-MP3212

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Components

#1: Protein urocanate hydratase


Mass: 58530.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: R450A mutant / Source: (gene. exp.) Variovorax sp. RA8 (bacteria) / Gene: hutU_2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P2DXK2
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 151 / Source method: isolated from a natural source / Formula: H2O
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: 3.35 Å3/Da / Density % sol: 63.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium sulfate 0.1 M Bis Tris propane, pH 7.5 20 % w/v PEG 3350

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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: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→49.27 Å / Num. obs: 1080243 / % possible obs: 100 % / Redundancy: 1 % / CC1/2: 0.998 / Net I/σ(I): 16.9
Reflection shellResolution: 2→2.05 Å / Num. unique obs: 78203 / CC1/2: 0.55

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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→49.27 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 29.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2685 5054 4.92 %
Rwork0.2407 --
obs0.2421 102801 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→49.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4053 0 44 151 4248
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054200
X-RAY DIFFRACTIONf_angle_d0.7895705
X-RAY DIFFRACTIONf_dihedral_angle_d16.895616
X-RAY DIFFRACTIONf_chiral_restr0.05637
X-RAY DIFFRACTIONf_plane_restr0.004749
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.38061600.3483210X-RAY DIFFRACTION100
2.02-2.050.32992020.32913242X-RAY DIFFRACTION100
2.05-2.070.37781640.31863239X-RAY DIFFRACTION100
2.07-2.10.341640.30433313X-RAY DIFFRACTION100
2.1-2.130.33151680.30933230X-RAY DIFFRACTION100
2.13-2.150.35391520.2993265X-RAY DIFFRACTION100
2.15-2.190.30971660.28683267X-RAY DIFFRACTION100
2.19-2.220.33381600.28973258X-RAY DIFFRACTION100
2.22-2.250.33341840.27683242X-RAY DIFFRACTION100
2.25-2.290.33051760.27793285X-RAY DIFFRACTION100
2.29-2.330.34761920.27983206X-RAY DIFFRACTION100
2.33-2.370.32851420.27663287X-RAY DIFFRACTION100
2.37-2.420.30611960.26723245X-RAY DIFFRACTION100
2.42-2.470.34151660.26893273X-RAY DIFFRACTION100
2.47-2.520.32182200.26223217X-RAY DIFFRACTION100
2.52-2.580.3311940.27063193X-RAY DIFFRACTION100
2.58-2.640.29741520.25333273X-RAY DIFFRACTION100
2.64-2.710.37761540.2553281X-RAY DIFFRACTION100
2.71-2.790.29211720.24193281X-RAY DIFFRACTION100
2.79-2.880.30091200.25613320X-RAY DIFFRACTION100
2.88-2.990.30381370.2463264X-RAY DIFFRACTION100
2.99-3.110.26751310.24063299X-RAY DIFFRACTION100
3.11-3.250.25351720.23613239X-RAY DIFFRACTION100
3.25-3.420.30671680.24423301X-RAY DIFFRACTION100
3.42-3.630.26821860.2353204X-RAY DIFFRACTION100
3.63-3.910.23671740.23283262X-RAY DIFFRACTION100
3.91-4.310.22782120.22293228X-RAY DIFFRACTION100
4.31-4.930.24811720.21743256X-RAY DIFFRACTION100
4.93-6.210.21011480.22143266X-RAY DIFFRACTION100
6.21-49.270.20231500.20963301X-RAY DIFFRACTION100

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