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- PDB-3o7j: Crystal structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazolin... -

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Basic information

Entry
Database: PDB / ID: 3o7j
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
1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9892
Polymers20,8331
Non-polymers1561
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.182, 47.317, 50.208
Angle α, β, γ (deg.)90.00, 123.13, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-185-

HOH

21A-201-

HOH

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Components

#1: Protein OHCU decarboxylase


Mass: 20833.295 Da / Num. of mol.: 1
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: Chemical ChemComp-2AL / 1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / ALLANTOIN


Mass: 156.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N4O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22-26% PEG-8000, 0.25 M sodium acetate in pH 6.5 cacodylate, 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: 2→50 Å / Num. all: 12300 / Num. obs: 12100 / % possible obs: 98.6 % / Observed criterion σ(I): 2 / Redundancy: 2.4 % / Rsym value: 0.076 / Net I/σ(I): 16.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.6 / Num. unique all: 560 / Rsym value: 0.263 / % possible all: 94.1

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q37

2q37


Resolution: 2→25.61 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.915 / SU B: 4.809 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24252 576 4.8 %RANDOM
Rwork0.21304 ---
obs0.21454 11525 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.162 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.09 Å2
2--0.06 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→25.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1270 0 11 89 1370
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0211298
X-RAY DIFFRACTIONr_angle_refined_deg0.9911.9721752
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8345165
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60323.17563
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.77315223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0191516
X-RAY DIFFRACTIONr_chiral_restr0.0550.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211001
X-RAY DIFFRACTIONr_mcbond_it0.3551.5824
X-RAY DIFFRACTIONr_mcangle_it0.70721297
X-RAY DIFFRACTIONr_scbond_it1.0423474
X-RAY DIFFRACTIONr_scangle_it1.8854.5455
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 39 -
Rwork0.269 812 -
obs--94.14 %

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