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- PDB-2h1x: Crystal structure of 5-hydroxyisourate Hydrolase (formerly known ... -

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Basic information

Entry
Database: PDB / ID: 2h1x
TitleCrystal structure of 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)
Components5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)
KeywordsHYDROLASE / 5-hydroxyisourate Hydrolase / TRP / uric acid degradation / allantoin
Function / homology
Function and homology information


ec:3.5.2.17: / hydroxyisourate hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / urate catabolic process / purine nucleobase metabolic process / peroxisome
Transthyretin/hydroxyisourate hydrolase / Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Transthyretin signature 1.
5-hydroxyisourate hydrolase / 5-hydroxyisourate hydrolase
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsZanotti, G. / Cendron, L. / Folli, C. / Ramazzina, I. / Percudani, R. / Berni, R.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Structure of Zebra fish HIUase: Insights into Evolution of an Enzyme to a Hormone Transporter.
Authors: Zanotti, G. / Cendron, L. / Ramazzina, I. / Folli, C. / Percudani, R. / Berni, R.
#1: Journal: NAT.CHEM.BIOL. / Year: 2006
Title: Completing the uric acid degradation pathway through phylogenetic comparison of whole genomes
Authors: Ramazzina, I. / Folli, C. / Secchi, A. / Berni, R. / Percudani, R.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 17, 2006 / Release: Oct 31, 2006
RevisionDateData content typeGroupProviderType
1.0Oct 31, 2006Structure modelrepositoryInitial release
1.1May 1, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Assembly

Deposited unit
A: 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)
B: 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)
C: 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)
D: 5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers53,0414
Non-polymers00
Water2,180121
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-40 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)58.078, 64.135, 58.937
Angle α, β, γ (deg.)90.00, 94.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 7 - 119 / Label seq-ID: 7 - 119

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
DetailsThe homo-tetramer present in the asymmetric unit coincides with the biological assembly

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Components

#1: Protein/peptide
5-hydroxyisourate Hydrolase (formerly known as TRP, Transthyretin Related Protein)


Mass: 13260.125 Da / Num. of mol.: 4 / Mutation: S2A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: GeneID:558664 / Plasmid: pET28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q0P422, UniProt: Q06S87*PLUS, EC: 3.5.2.17
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 121 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M HEPES, 20% PEG 10000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.91 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 7, 2006 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 1.98→500 Å / Num. all: 26947 / Num. obs: 26947 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.9
Reflection shellResolution: 1.98→2.09 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.19 / Mean I/σ(I) obs: 3.5 / Num. unique all: 3574 / % possible all: 89.1

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F41
Resolution: 1.98→58.82 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.918 / SU B: 4.35 / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0.19 / ESU R: 0.252 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25168 1367 5.1 %RANDOM
Rwork0.2057 ---
All0.20809 26946 --
Obs0.20809 25579 89.16 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å20 Å20.61 Å2
2--0.23 Å20 Å2
3---0.3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 1.98→58.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3572 0 0 121 3693
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0080.0223672
r_bond_other_d
r_angle_refined_deg1.1591.9435016
r_angle_other_deg
r_dihedral_angle_1_deg5.6035448
r_dihedral_angle_2_deg35.69422.821156
r_dihedral_angle_3_deg14.1515560
r_dihedral_angle_4_deg27.6021520
r_chiral_restr0.0760.2568
r_gen_planes_refined0.0040.022800
r_gen_planes_other
r_nbd_refined0.2340.31563
r_nbd_other
r_nbtor_refined0.3270.52516
r_nbtor_other
r_xyhbond_nbd_refined0.2180.5343
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.3010.357
r_symmetry_vdw_other
r_symmetry_hbond_refined0.260.516
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it2.21822320
r_mcbond_other
r_mcangle_it3.12633668
r_scbond_it2.34921584
r_scangle_it3.32231348
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

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

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A452medium positional0.220.5
2B452medium positional0.190.5
3C452medium positional0.190.5
4D452medium positional0.230.5
1A441loose positional0.365
2B441loose positional0.375
3C441loose positional0.415
4D441loose positional0.425
1A452medium thermal0.92
2B452medium thermal0.932
3C452medium thermal0.912
4D452medium thermal0.842
1A441loose thermal2.0710
2B441loose thermal1.8710
3C441loose thermal2.0110
4D441loose thermal1.9110
LS refinement shellResolution: 1.98→2.031 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 89 -
Rwork0.184 1644 -
Obs--78.52 %

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