[English] 日本語
Yorodumi
- PDB-3q1e: Crystal structure of Y116T/I16A double mutant of 5-hydroxyisourat... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3q1e
TitleCrystal structure of Y116T/I16A double mutant of 5-hydroxyisourate hydrolase in complex with T4
Components5-hydroxyisourate hydrolase
KeywordsHYDROLASE / HIUASE / TRANSTHYRETIN / TRP / THYROID HORMONES / MOLECULAR EVOLUTION / PURINE METABOLISM / Greek key beta-barrel / Point Mutation / peroxisome
Function / homology
Function and homology information


hydroxyisourate hydrolase / hydroxyisourate hydrolase activity / urate catabolic process / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides / 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
3,5,3',5'-TETRAIODO-L-THYRONINE / 5-hydroxyisourate hydrolase
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsCendron, L. / Ramazzina, I. / Percudani, R. / Zanotti, G. / Berni, R.
Citation
Journal: J.Mol.Biol. / Year: 2011
Title: Probing the evolution of hydroxyisourate hydrolase into transthyretin through active-site redesign.
Authors: Cendron, L. / Ramazzina, I. / Percudani, R. / Rasore, C. / Zanotti, G. / Berni, R.
#1: 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.
History
DepositionDec 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 4, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 1, 2020Group: Database references / Category: citation / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _struct_ref_seq_dif.details
Revision 1.3Nov 1, 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.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Advisory / Data collection
Category: chem_comp_atom / chem_comp_bond / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _pdbx_unobs_or_zero_occ_atoms.auth_atom_id / _pdbx_unobs_or_zero_occ_atoms.label_atom_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 5-hydroxyisourate hydrolase
B: 5-hydroxyisourate hydrolase
C: 5-hydroxyisourate hydrolase
D: 5-hydroxyisourate hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,2426
Polymers52,6884
Non-polymers1,5542
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-37 kcal/mol
Surface area19800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.771, 103.462, 53.490
Angle α, β, γ (deg.)90.00, 109.47, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1 / Refine code: 5

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA7 - 337 - 33
21SERSERASPASPBB7 - 337 - 33
31SERSERASPASPCC7 - 337 - 33
41SERSERASPASPDD7 - 337 - 33
12THRTHRPROPROAA44 - 5444 - 54
22THRTHRPROPROBB44 - 5444 - 54
32THRTHRPROPROCC44 - 5444 - 54
42THRTHRPROPRODD44 - 5444 - 54
13PHEPHETHRTHRAA62 - 11562 - 115
23PHEPHETHRTHRBB62 - 11562 - 115
33PHEPHETHRTHRCC62 - 11562 - 115
43PHEPHETHRTHRDD62 - 11562 - 115

-
Components

#1: Protein
5-hydroxyisourate hydrolase / HIU hydrolase / HIUHase / Transthyretin-related protein


Mass: 13171.975 Da / Num. of mol.: 4 / Fragment: residues in UNP 20-138 / Mutation: Y116T, I16A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: urah / Plasmid: PET28B-HIUASE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q06S87, hydroxyisourate hydrolase
#2: Chemical ChemComp-T44 / 3,5,3',5'-TETRAIODO-L-THYRONINE


Mass: 776.870 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H11I4NO4 / Comment: hormone*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 278 K / Method: vapor diffusion / pH: 7.5
Details: 0.1M HEPES, 20% PEG 10000, pH 7.5, VAPOR DIFFUSION, temperature 278K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2009 / Details: SI(111) and Pt coated mirrors in KB geometry
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 1.95→51.73 Å / Num. all: 33889 / Num. obs: 33889 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 9.5
Reflection shellResolution: 1.95→2.06 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.458 / Mean I/σ(I) obs: 2.1 / Num. unique all: 4721 / % possible all: 94.3

-
Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MLPHAREphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IWU

3iwu


Resolution: 1.95→51.73 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.923 / SU B: 13.498 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R Free: 0.182 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27116 1717 5.1 %RANDOM
Rwork0.22227 ---
all0.22489 33863 --
obs0.22489 33863 98.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 43.866 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å20 Å22.88 Å2
2---1.58 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 1.95→51.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3579 0 10 55 3644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0223675
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9071.9455022
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6975453
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.25222.895152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.76815561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0841520
X-RAY DIFFRACTIONr_chiral_restr0.1290.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212788
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9031.52273
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.47723705
X-RAY DIFFRACTIONr_scbond_it2.55431402
X-RAY DIFFRACTIONr_scangle_it3.7614.51317
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A368medium positional0.170.5
B368medium positional0.160.5
C368medium positional0.190.5
D368medium positional0.190.5
A359loose positional0.475
B359loose positional0.485
C359loose positional0.425
D359loose positional0.455
A368medium thermal1.092
B368medium thermal0.982
C368medium thermal1.22
D368medium thermal0.992
A359loose thermal1.4510
B359loose thermal1.4610
C359loose thermal1.6410
D359loose thermal1.4210
LS refinement shellResolution: 1.95→2.001 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 100 -
Rwork0.317 2155 -
obs--89.13 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.45250.3445-0.08951.8408-0.27561.3147-0.15850.2301-0.0369-0.23860.14430.08020.082-0.09580.01420.21440.008-0.02880.18920.00790.15360.270512.047912.8446
24.69611.61945.31081.96260.6347.257-0.1174-0.14050.0585-0.0272-0.0107-0.1315-0.4478-0.23340.12810.36970.01140.06280.16350.01780.226213.24325.37724.1176
33.38011.47380.72326.46042.12652.8717-0.06550.1734-0.0951-0.19830.06870.0005-0.03950.1243-0.00320.25660.0070.00290.23470.02310.20272.411615.96848.2808
48.0665-0.1916-0.24961.5512-1.38674.8466-0.11290.447-0.0227-0.4517-0.0751-0.4359-0.32640.23530.1880.3532-0.04420.09020.090.00360.242316.390719.788516.5973
51.6599-0.07940.0461.4950.17551.76960.08820.08610.0864-0.1152-0.0311-0.0392-0.11050.0036-0.05710.23350.0018-0.0160.17020.010.1882.068614.064420.0431
61.2518-0.24880.97013.1368-0.32681.9702-0.03610.2298-0.16-0.26560.0103-0.15910.04060.08640.02580.2341-0.0074-0.03480.1765-0.00910.18230.50986.75820.4613
78.9912-3.9222-5.17134.74741.41683.2312-0.2422-0.1932-0.19990.16820.17470.28610.20890.0940.06750.24930.001-0.0350.20370.01740.1746-0.6082.731238.6138
81.2385-1.258-0.14775.0571-0.60081.2989-0.0316-0.01870.14110.12760.0018-0.10.0133-0.04520.02980.19330.0105-0.04970.22390.01970.17722.107915.218739.2221
98.34511.1711-0.64962.7669-0.66964.1117-0.0562-0.0314-0.22960.09140.0590.04690.1444-0.0144-0.00280.23370.0086-0.01050.220.01610.1953.39261.417343.9613
102.48110.2925-1.04951.8581-1.61894.18140.0247-0.236-0.0620.50130.05880.2631-0.1642-0.1789-0.08350.2138-0.0007-0.00170.17770.00330.1919-7.6115.48942.0444
111.6949-0.3322-0.44792.1721-0.22521.8713-0.0556-0.1108-0.10470.08680.0359-0.05340.01110.12090.01970.2302-0.0162-0.05150.20410.00280.1853.93759.372233.8368
125.818-0.6259-1.27943.34250.26163.6618-0.1337-0.0924-0.23370.18050.07830.09530.1712-0.13050.05540.2102-0.0062-0.03250.17980.01420.17642.44453.780829.4059
132.89830.62590.30461.3814-1.37361.7058-0.00120.1140.203-0.032-0.0951-0.039-0.00890.17670.09620.2288-0.04530.01350.1946-0.02340.23376.9645-4.40799.0198
140.9257-0.5243-0.35641.78280.17982.86920.1629-0.0744-0.1656-0.0957-0.08820.02670.194-0.0391-0.07470.18230.03540.02220.22450.01870.2062.9433-15.13198.7755
151.3460.540.18130.9233-0.23552.54730.02490.03520.0021-0.2555-0.0383-0.0627-0.06680.10240.01340.15310.02080.0180.1976-0.0170.2156.4867-11.93983.8063
163.27341.33530.40952.3686-2.83375.2955-0.11480.37550.2076-0.22880.09720.09690.0505-0.01680.01760.23820.048-0.00930.2299-0.00260.2074-4.3032-13.14811.452
171.08220.0966-0.75931.6363-0.04571.8815-0.03570.02780.027-0.0461-0.0059-0.03450.03270.16590.04160.1582-0.0060.0080.1902-0.01350.21293.935-11.159814.1975
184.2041-0.69631.27532.94010.20094.5675-0.10770.14690.181-0.0661-0.0119-0.0522-0.24960.17690.11960.1465-0.02170.0140.2051-0.01740.23633.57-5.337319.1812
191.8306-0.72690.46120.9226-1.91275.1916-0.0254-0.1399-0.02880.09480.00360.0594-0.0028-0.02070.02180.2377-0.01710.05280.204-0.03660.2166-8.5898-11.007934.4125
202.3629-2.1099-0.64923.85260.56891.65960.0720.0382-0.1554-0.0048-0.0647-0.01310.219-0.0337-0.00730.141-0.01350.02230.21410.00860.2517-7.3009-20.345425.5768
213.4933-1.9235-0.34778.0685-0.17313.4091-0.0397-0.1570.07420.20410.01080.0188-0.092-0.05150.02890.1887-0.00670.02080.24080.00490.2183-14.7966-12.094733.2357
223.10450.71461.42341.07221.41361.9529-0.0859-0.544-0.34880.2931-0.02630.16390.3384-0.11150.11220.22830.0730.1120.21070.03480.2428-2.7356-23.826533.4029
231.3367-0.1429-0.28081.70830.19152.1436-0.0322-0.0935-0.05580.09130.03040.12620.0431-0.15580.00180.147-0.01740.01670.1935-0.01780.2267-6.9434-12.420424.0292
244.5798-0.81320.67354.2292-0.75253.7012-0.0667-0.3037-0.04570.18210.08220.064-0.1875-0.0447-0.01550.1218-0.01110.01120.1774-0.02560.2219-4.1944-5.248723.3441
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 29
2X-RAY DIFFRACTION2A30 - 43
3X-RAY DIFFRACTION3A44 - 56
4X-RAY DIFFRACTION4A57 - 69
5X-RAY DIFFRACTION5A70 - 104
6X-RAY DIFFRACTION6A105 - 119
7X-RAY DIFFRACTION7B6 - 17
8X-RAY DIFFRACTION8B18 - 45
9X-RAY DIFFRACTION9B46 - 54
10X-RAY DIFFRACTION10B55 - 69
11X-RAY DIFFRACTION11B70 - 103
12X-RAY DIFFRACTION12B104 - 119
13X-RAY DIFFRACTION13C6 - 17
14X-RAY DIFFRACTION14C18 - 38
15X-RAY DIFFRACTION15C39 - 59
16X-RAY DIFFRACTION16C60 - 69
17X-RAY DIFFRACTION17C70 - 106
18X-RAY DIFFRACTION18C107 - 119
19X-RAY DIFFRACTION19D4 - 17
20X-RAY DIFFRACTION20D18 - 43
21X-RAY DIFFRACTION21D44 - 55
22X-RAY DIFFRACTION22D56 - 69
23X-RAY DIFFRACTION23D70 - 106
24X-RAY DIFFRACTION24D107 - 119

+
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