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- PDB-2o73: Structure of OHCU decarboxylase in complex with allantoin -

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Basic information

Entry
Database: PDB / ID: 2o73
TitleStructure of OHCU decarboxylase in complex with allantoin
ComponentsOHCU decarboxylase
KeywordsLYASE / Decarboxylation / OHCU / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline / HIU / 5-hydroxyisourate
Function / homology
Function and homology information


2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase activity / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / urate catabolic process / allantoin metabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
UraD-like / Oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase, type 1 / 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 speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsCendron, L. / Berni, R. / Folli, C. / Ramazzina, I. / Percudani, R. / Zanotti, G.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: The structure of 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase provides insights into the mechanism of uric acid degradation.
Authors: Cendron, L. / Berni, R. / Folli, C. / Ramazzina, I. / Percudani, R. / Zanotti, G.
History
DepositionDec 10, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 2, 2014Group: Database references
Revision 1.4Oct 25, 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 / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _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

Downloads & links

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Assembly

Deposited unit
A: OHCU decarboxylase
B: OHCU decarboxylase
C: OHCU decarboxylase
D: OHCU decarboxylase
E: OHCU decarboxylase
F: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,54812
Polymers118,6126
Non-polymers9376
Water9,908550
1
A: OHCU decarboxylase
B: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8494
Polymers39,5372
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-12 kcal/mol
Surface area15120 Å2
MethodPISA
2
C: OHCU decarboxylase
D: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8494
Polymers39,5372
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-13 kcal/mol
Surface area15340 Å2
MethodPISA
3
E: OHCU decarboxylase
F: OHCU decarboxylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8494
Polymers39,5372
Non-polymers3122
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-13 kcal/mol
Surface area15370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.212, 102.212, 103.868
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASP / Beg label comp-ID: ASP / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 2 - 164 / Label seq-ID: 2 - 164

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe enzyme in solution is a dimer, there are three dimers in the asymmetric unit (AB, CD, EF)

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Components

#1: Protein
OHCU decarboxylase / 2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase


Mass: 19768.645 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: zgc:158663 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A1L259
#2: Chemical
ChemComp-2AL / 1-(2,5-DIOXO-2,5-DIHYDRO-1H-IMIDAZOL-4-YL)UREA / ALLANTOIN / Allantoin


Mass: 156.100 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H4N4O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.64 Å3/Da / Density % sol: 53.41 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 8.5
Details: 20% (v/v) EtOH, 100mM TrisHCl, pH 8.5, VAPOR DIFFUSION, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 29, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.8→88.39 Å / Num. all: 104588 / Num. obs: 104588 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.5
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 1.7 / Num. unique all: 11935 / % possible all: 72.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2O70

2o70


Resolution: 1.8→83 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.92 / SU B: 3.084 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.45 / ESU R: 0.147 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25151 5205 5 %RANDOM
Rwork0.21703 ---
all0.21876 99340 --
obs0.21876 99340 92.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.034 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.8→83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 66 550 8511
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228102
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1991.97710934
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0165986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.30223.846390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.485151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8941572
X-RAY DIFFRACTIONr_chiral_restr0.0810.21231
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026110
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2320.34317
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.310.55764
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2060.51017
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2010.366
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.10225155
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.66838071
X-RAY DIFFRACTIONr_scbond_it1.25623273
X-RAY DIFFRACTIONr_scangle_it1.91432863
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A652medium positional0.290.5
2B652medium positional0.190.5
3C652medium positional0.340.5
4D652medium positional0.20.5
5E652medium positional0.210.5
6F652medium positional0.180.5
1A647loose positional0.75
2B647loose positional0.75
3C647loose positional0.815
4D647loose positional0.675
5E647loose positional0.715
6F647loose positional0.755
1A652medium thermal2.362
2B652medium thermal1.392
3C652medium thermal2.732
4D652medium thermal1.182
5E652medium thermal1.82
6F652medium thermal2.522
1A647loose thermal3.3510
2B647loose thermal2.2410
3C647loose thermal4.0810
4D647loose thermal1.9210
5E647loose thermal2.5110
6F647loose thermal3.6810
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 281 -
Rwork0.338 5361 -
obs--68.09 %

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