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- PDB-2o70: Structure of OHCU decarboxylase from zebrafish -

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Basic information

Entry
Database: PDB / ID: 2o70
TitleStructure of OHCU decarboxylase from zebrafish
ComponentsOHCU decarboxylase
KeywordsLYASE / Uric acid / decarboxylation / 5-hydroxyisourate / allantoin
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 / 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
2-oxo-4-hydroxy-4-carboxy-5-ureidoimidazoline decarboxylase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / 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 9, 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 1.4Dec 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
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

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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


Theoretical massNumber of molelcules
Total (without water)118,6126
Polymers118,6126
Non-polymers00
Water22,0501224
1
A: OHCU decarboxylase
B: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-14 kcal/mol
Surface area15390 Å2
MethodPISA
2
C: OHCU decarboxylase
D: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2260 Å2
ΔGint-14 kcal/mol
Surface area15610 Å2
MethodPISA
3
E: OHCU decarboxylase
F: OHCU decarboxylase


Theoretical massNumber of molelcules
Total (without water)39,5372
Polymers39,5372
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-14 kcal/mol
Surface area15500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.815, 101.815, 103.915
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: ILE / End label comp-ID: ILE / Refine code: 5 / Auth seq-ID: 2 - 165 / Label seq-ID: 2 - 165

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
DetailsThe biological unit is a dimer. There are three dimers in the asymmetric unit.

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1224 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 8.5
Details: 20 % (v/v) EtOH, 100mM TrisHCl, pH 8.5, VAPOR DIFFUSION, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID2911.07225
SYNCHROTRONESRF ID2920.97878, 0.97891, 0.97604
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDJul 6, 2006
ADSC QUANTUM 3152CCDSep 29, 2006
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.072251
20.978781
30.978911
40.976041
ReflectionResolution: 1.8→103.69 Å / Num. all: 111211 / Num. obs: 111211 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 17.4
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.8 / Num. unique all: 16284 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCQUANTUMdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→67 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.989 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.13 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24022 5572 5 %RANDOM
Rwork0.19553 ---
all0.19777 105633 --
obs0.19777 105633 99.56 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.501 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.8→67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7895 0 0 1224 9119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0228036
X-RAY DIFFRACTIONr_angle_refined_deg1.1671.9710844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425986
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.5723.846390
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.316151478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2361572
X-RAY DIFFRACTIONr_chiral_restr0.0770.21225
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026038
X-RAY DIFFRACTIONr_nbd_refined0.2310.34298
X-RAY DIFFRACTIONr_nbtor_refined0.3120.55764
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2110.51493
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1930.375
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3010.553
X-RAY DIFFRACTIONr_mcbond_it1.14225111
X-RAY DIFFRACTIONr_mcangle_it1.73838005
X-RAY DIFFRACTIONr_scbond_it1.3523239
X-RAY DIFFRACTIONr_scangle_it2.07832839
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A656medium positional0.230.5
2B656medium positional0.190.5
3C656medium positional0.370.5
4D656medium positional0.260.5
5E656medium positional0.220.5
6F656medium positional0.190.5
1A651loose positional0.685
2B651loose positional0.675
3C651loose positional0.815
4D651loose positional0.65
5E651loose positional0.655
6F651loose positional0.645
1A656medium thermal1.522
2B656medium thermal1.382
3C656medium thermal2.882
4D656medium thermal1.212
5E656medium thermal2.352
6F656medium thermal2.352
1A651loose thermal2.3810
2B651loose thermal2.0810
3C651loose thermal3.9110
4D651loose thermal2.0810
5E651loose thermal3.1810
6F651loose thermal3.410
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 391 -
Rwork0.267 7466 -
obs--95.16 %

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