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- PDB-2fkn: crystal structure of urocanase from bacillus subtilis -

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Basic information

Entry
Database: PDB / ID: 2fkn
Titlecrystal structure of urocanase from bacillus subtilis
ComponentsUrocanate hydratase
KeywordsLYASE / rossmann fold
Function / homology
Function and homology information


urocanate hydratase / urocanate hydratase activity / L-histidine catabolic process / 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
ACETATE ION / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Urocanate hydratase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYu, Y.-M. / Liang, Y.-H. / Su, X.-D.
CitationJournal: To be Published
Title: Crystal Structure of Urocanase from Bacillus Subtilis
Authors: Yu, Y.-M. / Liang, Y.-H. / Su, X.-D.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 2, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.5Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urocanate hydratase
B: Urocanate hydratase
C: Urocanate hydratase
D: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,60212
Polymers242,7124
Non-polymers2,8908
Water10,413578
1
A: Urocanate hydratase
B: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8016
Polymers121,3562
Non-polymers1,4454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-72 kcal/mol
Surface area33270 Å2
MethodPISA
2
C: Urocanate hydratase
D: Urocanate hydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8016
Polymers121,3562
Non-polymers1,4454
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-73 kcal/mol
Surface area32950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.791, 131.268, 164.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Urocanate hydratase / Urocanase / Imidazolonepropionate hydrolase


Mass: 60678.078 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: hutU / Plasmid: pet28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21(de3) / References: UniProt: P25503, urocanate hydratase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 578 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2m Ammonium acetate, 0.1m Tris, 25% Polyethylene glycol 3350, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9913
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 4, 2005
RadiationMonochromator: SI 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9913 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 107286 / % possible obs: 97 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.064
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.335 / % possible all: 91.6

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Processing

Software
NameVersionClassification
MAR345data collection
HLKdata reduction
PHASERphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: engh & huber
RfactorNum. reflection% reflectionSelection details
Rfree0.256 5350 4.9 %RANDOM
Rwork0.205 ---
obs0.205 107159 97.3 %-
Solvent computationBsol: 32.36 Å2
Displacement parametersBiso mean: 28.18 Å2
Baniso -1Baniso -2Baniso -3
1-4.925 Å20 Å20 Å2
2---17.302 Å20 Å2
3---12.377 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16798 0 192 578 17568
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.34
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2water_rep.param
X-RAY DIFFRACTION3nad_xplor_par.txt
X-RAY DIFFRACTION4act.param

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