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- PDB-1uwl: 1.76A Structure of Urocanate Hydratase from Pseudomonas putida -

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Basic information

Entry
Database: PDB / ID: 1uwl
Title1.76A Structure of Urocanate Hydratase from Pseudomonas putida
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 / Urocanate hydratase
Similarity search - Component
Biological speciesPSEUDOMONAS PUTIDA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 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 1.3Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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)122,9824
Polymers121,6552
Non-polymers1,3272
Water15,295849
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8800 Å2
ΔGint-62.52 kcal/mol
Surface area31940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.430, 71.622, 129.120
Angle α, β, γ (deg.)90.00, 98.99, 90.00
Int Tables number5
Space group name H-MC121
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: 60827.535 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: CONTAINING NAD+ / Source: (gene. exp.) PSEUDOMONAS PUTIDA (bacteria) / Plasmid: BL21 DE3 / Production host: ESCHERICHIA COLI (E. coli) / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION CYS 197 SER CHAINS A AND B. CATALYSES THE CONVERSION OF 3-(5-OXO-4,5-DIHYDRO-3- ...ENGINEERED MUTATION CYS 197 SER 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 ANNONTATED IN THE RECORDS BELOW HAVE BEEN DOCUMENTED IN UNIPROT AND DEPOSITED BY S.L. ...THE CONFLICT ANNONTATED 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: 2 Å3/Da / Density % sol: 43 %
Crystal growpH: 5.8 / Details: pH 5.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.89,0.9824,0.9820,0.9103
DetectorDate: Feb 15, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.891
20.98241
30.9821
40.91031
ReflectionResolution: 1.76→30 Å / Num. obs: 47378 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 14.4
Reflection shellResolution: 1.76→1.8 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 5.1 / % possible all: 94

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Processing

Software
NameClassification
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.76→24.33 Å / SU B: 2.203 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.123 / ESU R Free: 0.107 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1886 4924 5 %RANDOM
Rwork0.1682 ---
obs0.16924 93721 99 %-
Displacement parametersBiso mean: 12.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.31 Å20 Å20.19 Å2
2---0.01 Å20 Å2
3---0.37 Å2
Refinement stepCycle: LAST / Resolution: 1.76→24.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8445 0 88 849 9382

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