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- PDB-2h6u: Crystal structure of 5-hydroxyisourate hydrolase (formerly known ... -

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Basic information

Entry
Database: PDB / ID: 2h6u
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


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / urate catabolic process / purine nucleobase metabolic process / peroxisome
Similarity search - Function
Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like ...Hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
5-hydroxyisourate hydrolase / 5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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.
History
DepositionJun 1, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _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: 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)
E: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
F: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
G: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
H: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)


Theoretical massNumber of molelcules
Total (without water)106,0818
Polymers106,0818
Non-polymers00
Water10,773598
1
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
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6100 Å2
ΔGint-45 kcal/mol
Surface area19010 Å2
MethodPISA, PQS
2
E: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
F: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
G: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)
H: 5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)


Theoretical massNumber of molelcules
Total (without water)53,0414
Polymers53,0414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-43 kcal/mol
Surface area18970 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)64.324, 66.737, 237.393
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 6 / Auth seq-ID: 6 - 119 / Label seq-ID: 6 - 119

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
DetailsThe biological unit is a homo-tetramer. Two of such tetramers are present in the asymmetric unit.

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Components

#1: Protein
5-HYDROXYISOURATE HYDROLASE (FORMERLY KNOWN AS TRP, TRANSTHYRETIN RELATED PROTEIN)


Mass: 13260.125 Da / Num. of mol.: 8 / Mutation: S2A, P6L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: GENEID:558664 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3)
References: UniProt: Q0P422, UniProt: Q06S87*PLUS, hydroxyisourate hydrolase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 598 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20% (w/v) PEG 10000, 0.1 M Hepes, 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: ID14-1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.7→118 Å / Num. all: 103601 / Num. obs: 103601 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.8 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 7.2
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.236 / Mean I/σ(I) obs: 3 / Num. unique all: 12933 / % possible all: 80.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCdata collection
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2H1X

2h1x


Resolution: 1.7→64.2 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.915 / SU B: 2.553 / SU ML: 0.086 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.136 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25493 5163 5 %RANDOM
Rwork0.2238 ---
all0.22537 103553 --
obs0.22537 98390 91.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.467 Å2
Baniso -1Baniso -2Baniso -3
1--0.27 Å20 Å20 Å2
2--0.19 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→64.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7208 0 0 598 7806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0227408
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2061.94610120
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4575904
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.39722.821312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.327151136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.2471540
X-RAY DIFFRACTIONr_chiral_restr0.0840.21152
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2090.33214
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3230.55077
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.51019
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2760.338
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1450.523
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.34824686
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.99837400
X-RAY DIFFRACTIONr_scbond_it1.44923194
X-RAY DIFFRACTIONr_scangle_it2.09232720
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 901 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.245
2Bloose positional0.35
3Cloose positional0.255
4Dloose positional0.225
5Eloose positional0.265
6Floose positional0.435
7Gloose positional0.255
8Hloose positional0.295
1Aloose thermal4.0410
2Bloose thermal3.9110
3Cloose thermal2.410
4Dloose thermal2.9310
5Eloose thermal3.4510
6Floose thermal3.510
7Gloose thermal3.5110
8Hloose thermal2.4910
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 298 -
Rwork0.29 5716 -
obs--72.54 %

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