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- PDB-1uwk: The High Resolution Structure of Urocanate Hydratase from Pseudom... -

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Basic information

Entry
Database: PDB / ID: 1uwk
TitleThe High Resolution Structure of Urocanate Hydratase from Pseudomonas putida in complex with urocanate
ComponentsUROCANATE HYDRATASE
KeywordsHYDROLASE / UROCANASE / IMIDAZOLONEPROPIONATE / HISTIDINE METABOLISM / LYASE
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 / cytoplasm
Similarity search - Function
Urocanase fold / Urocanase superfamily / Urocanase like domains / Urocanase conserved site / Urocanase signature. / Urocanase / Urocanase, Rossmann-like domain / Urocanase, N-terminal domain / Urocanase, C-terminal domain / Urocanase superfamily ...Urocanase fold / Urocanase superfamily / Urocanase like domains / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID / Urocanate hydratase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.19 Å
AuthorsKessler, D. / Retey, J. / Schulz, G.E.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: Structure and Action of Urocanase
Authors: Kessler, D. / Retey, J. / Schulz, G.E.
History
DepositionFeb 5, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 22, 2019Group: Data collection / Other / Refinement description
Category: pdbx_database_proc / pdbx_database_status / refine
Item: _pdbx_database_status.recvd_author_approval / _refine.pdbx_ls_cross_valid_method
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UROCANATE HYDRATASE
B: UROCANATE HYDRATASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,1186
Polymers121,5152
Non-polymers1,6034
Water15,133840
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)111.429, 71.618, 129.158
Angle α, β, γ (deg.)90.00, 98.75, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-2191-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.41275, -0.90295, -0.11969), (-0.90432, 0.39054, 0.17229), (-0.10882, 0.17935, -0.97775)
Vector: 41.12912, 34.95136, -66.13895)

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Components

#1: Protein UROCANATE HYDRATASE / UROCANASE / IMIDAZOLONEPROPIONATE HYDROLASE


Mass: 60757.480 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CONTAINING NAD+ AND UROCANATE / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P25080, urocanate hydratase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Chemical ChemComp-URO / (2E)-3-(1H-IMIDAZOL-4-YL)ACRYLIC ACID


Mass: 138.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H6N2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 840 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION CYS 198 SER AND ARG 455 ALA IN CHAINS A AND B. CATALYSES THE CONVERSION OF 3-(5- ...ENGINEERED MUTATION CYS 198 SER AND ARG 455 ALA IN CHAINS A AND B. CATALYSES THE CONVERSION OF 3-(5-OXO-4,5-DIHYDRO-3-H- IMIDAZOL-4-YL)PROPANOATE TO UROCANATE + H(2)O. MEMBER OF THE HISTIDINE DEGRADATION PATHWAY.
Sequence detailsTHE CONFLICT ANNOTATED IN THE RECORDS BELOW HAVE BEEN DOCUMENTED IN UNIPROT AND DEPOSITED BY S.L. ...THE CONFLICT ANNOTATED IN THE RECORDS BELOW HAVE BEEN DOCUMENTED IN UNIPROT AND DEPOSITED BY S.L.ALLISION AND A.T.PHILIPS (NOV-1993).

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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: 1.77 Å3/Da / Density % sol: 30.6 %
Crystal growpH: 5.8
Details: 24% PEG8000, 0.1M SODIUM CACODYLATE (PH 5.8), 0.16M SODIUM ACETATE, 0.1% BETA-MERCAPTOETHANOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0008
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0008 Å / Relative weight: 1
ReflectionResolution: 1.14→30 Å / Num. obs: 1453010 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 13
Reflection shellResolution: 1.14→1.21 Å / Redundancy: 3 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 2 / % possible all: 90

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.19→50 Å / Num. parameters: 85193 / Num. restraintsaints: 105344 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH / Details: ANISTROPIC REFINEMENT REDUCED FREE R
RfactorNum. reflection% reflectionSelection details
Rfree0.179 15948 5 %RANDOM
all0.141 302973 --
obs0.1396 -94.7 %-
Solvent computationSolvent model: MOEWS
Refine analyzeNum. disordered residues: 5 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 9465.5
Refinement stepCycle: LAST / Resolution: 1.19→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8479 0 108 840 9427
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.018
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0302
X-RAY DIFFRACTIONs_zero_chiral_vol0.069
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.075
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.093
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.004
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.041
X-RAY DIFFRACTIONs_approx_iso_adps0.068

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