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- PDB-3o7i: Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazolin... -

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Basic information

Entry
Database: PDB / ID: 3o7i
TitleCrystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase from Klebsiella pneumoniae
ComponentsOHCU decarboxylase
KeywordsLYASE / decarboxylase
Function / homology
Function and homology information


2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / urate catabolic process / purine nucleobase metabolic process
Similarity search - Function
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 2 / UraD-like / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase superfamily / OHCU decarboxylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFrench, J.B. / Ealick, S.E.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and Mechanistic Studies on Klebsiella pneumoniae 2-Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline Decarboxylase.
Authors: French, J.B. / Ealick, S.E.
History
DepositionJul 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: OHCU decarboxylase
B: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)41,6672
Polymers41,6672
Non-polymers00
Water11,764653
1
A: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)20,8331
Polymers20,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)20,8331
Polymers20,8331
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.179, 88.179, 40.217
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein OHCU decarboxylase


Mass: 20833.295 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae (bacteria)
Strain: ATCC 700721 / Gene: KPN78578_16350, KPN_01665 / Production host: Escherichia coli (E. coli) / References: UniProt: A6T925
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 1.88 Å3/Da / Density % sol: 34.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 20% PEG-3000, 0.2 M calcium acetate, pH 7.0 Tris-HCl, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jan 1, 2010
RadiationMonochromator: Horizontal focusing 5.05 asymmetric cut Si(111)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. all: 49900 / Num. obs: 49800 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 7.4 % / Rsym value: 0.096 / Net I/σ(I): 28.7
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 2462 / Rsym value: 0.37 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→29.39 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.926 / SU B: 1.364 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2292 2527 5.1 %RANDOM
Rwork0.20543 ---
obs0.20663 47279 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.786 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.5→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2296 0 0 653 2949
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0212335
X-RAY DIFFRACTIONr_angle_refined_deg0.8241.9723148
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9545295
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41223.103116
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3315412
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.9531530
X-RAY DIFFRACTIONr_chiral_restr0.0530.2351
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211786
X-RAY DIFFRACTIONr_mcbond_it0.1961.51478
X-RAY DIFFRACTIONr_mcangle_it0.41622327
X-RAY DIFFRACTIONr_scbond_it0.7483857
X-RAY DIFFRACTIONr_scangle_it1.3274.5821
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 185 -
Rwork0.228 3491 -
obs--99.92 %

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