[English] 日本語
Yorodumi
- PDB-2h1x: Crystal structure of 5-hydroxyisourate Hydrolase (formerly known ... -

+
Open data


ID or keywords:

Loading...

-
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


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: 1.98 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.
History
DepositionMay 17, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6210 Å2
ΔGint-40 kcal/mol
Surface area18530 Å2
MethodPISA
Unit cell
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 auth comp-ID: SER / Beg label comp-ID: SER / End auth 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

-
Components

#1: Protein
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, hydroxyisourate hydrolase
#2: Water ChemComp-HOH / water / Water


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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ADSCdata collection
MOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F41

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
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223672
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1591.9435016
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6035448
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69422.821156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.1515560
X-RAY DIFFRACTIONr_dihedral_angle_4_deg27.6021520
X-RAY DIFFRACTIONr_chiral_restr0.0760.2568
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022800
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2340.31563
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3270.52516
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.5343
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.357
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.260.516
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.21822320
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.12633668
X-RAY DIFFRACTIONr_scbond_it2.34921584
X-RAY DIFFRACTIONr_scangle_it3.32231348
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
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 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more