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- PDB-7ned: Thiourocanate hydratase from Paenibacillus sp. Soil724D2 in compl... -

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Basic information

Entry
Database: PDB / ID: 7ned
TitleThiourocanate hydratase from Paenibacillus sp. Soil724D2 in complex with cofactor NAD+ and urocanate
ComponentsUrocanate hydratase
KeywordsLYASE / thiourocanate hydratase / ergothioneine catabolism
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 / nucleotide binding / cytoplasm
Similarity search - Function
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 / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID / Urocanate hydratase
Similarity search - Component
Biological speciesPaenibacillus sp. Soil724D2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLeisinger, F. / Seebeck, F.P.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Acs Chem.Biol. / Year: 2021
Title: In Vitro Reconstitution of a Five-Step Pathway for Bacterial Ergothioneine Catabolism.
Authors: Beliaeva, M.A. / Leisinger, F. / Seebeck, F.P.
History
DepositionFeb 3, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2021Group: 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
Revision 1.2Jan 31, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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 hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,1314
Polymers60,2671
Non-polymers8643
Water4,882271
1
A: Urocanate hydratase
hetero molecules

A: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,2618
Polymers120,5342
Non-polymers1,7276
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area9670 Å2
ΔGint-60 kcal/mol
Surface area33980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.349, 62.747, 151.466
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Space group name HallP22ab(y,z,x)
Symmetry operation#1: x,y,z
#2: x+1/2,-y,-z+1/2
#3: -x,y,-z
#4: -x+1/2,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-1062-

HOH

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Components

#1: Protein Urocanate hydratase / Urocanase / Imidazolonepropionate hydrolase / thiourocanate hydratase


Mass: 60267.098 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus sp. Soil724D2 (bacteria) / Gene: hutU, ASG85_10330 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0Q9KFZ4, urocanate hydratase
#2: Chemical ChemComp-URO / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID


Mass: 138.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O2 / Feature type: SUBJECT OF INVESTIGATION
#3: 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
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 293.5 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: (NH4)2SO4, Bis-Tris-buffer

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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: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→48.32 Å / Num. obs: 41723 / % possible obs: 99.9 % / Redundancy: 10.3 % / CC1/2: 0.996 / Rmerge(I) obs: 0.212 / Rpim(I) all: 0.071 / Rrim(I) all: 0.224 / Net I/σ(I): 11.5 / Num. measured all: 429898 / Scaling rejects: 799
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
1.9-1.9410.21.3212722126650.7820.441.3942.5100
9.11-48.3290.04140544490.9990.0150.04433.299.5

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.18.2refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1w1u

1w1u


Resolution: 1.9→48.32 Å / SU ML: 0.1532 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 16.7369
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.175 2070 4.97 %
Rwork0.1716 39574 -
obs0.1718 41644 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.38 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 58 271 4561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01414372
X-RAY DIFFRACTIONf_angle_d1.38325932
X-RAY DIFFRACTIONf_chiral_restr0.0932659
X-RAY DIFFRACTIONf_plane_restr0.0092780
X-RAY DIFFRACTIONf_dihedral_angle_d23.12791588
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.940.2711490.23412580X-RAY DIFFRACTION99.89
1.94-1.990.22971470.21322567X-RAY DIFFRACTION99.82
1.99-2.050.21071260.20992592X-RAY DIFFRACTION99.82
2.05-2.110.23261560.18782596X-RAY DIFFRACTION100
2.11-2.170.20071230.18742639X-RAY DIFFRACTION99.89
2.17-2.250.1921520.17682576X-RAY DIFFRACTION99.89
2.25-2.340.18321290.17412616X-RAY DIFFRACTION100
2.34-2.450.19671420.17332631X-RAY DIFFRACTION99.82
2.45-2.580.20781280.17492636X-RAY DIFFRACTION99.86
2.58-2.740.15251140.17182641X-RAY DIFFRACTION99.78
2.74-2.950.17281420.18092610X-RAY DIFFRACTION99.71
2.95-3.250.14671380.17682653X-RAY DIFFRACTION99.93
3.25-3.720.16671370.16492689X-RAY DIFFRACTION99.89
3.72-4.680.14681110.13882732X-RAY DIFFRACTION100
4.69-48.320.14891760.16232816X-RAY DIFFRACTION99.73

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