[English] 日本語
Yorodumi
- PDB-7rlk: Wallaby TTR -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rlk
TitleWallaby TTR
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Transthyretin / Thyroxine
Function / homology
Function and homology information


thyroid hormone transport / retinol metabolic process / thyroid hormone binding / hormone activity / extracellular region
Similarity search - Function
Transthyretin / Transthyretin, conserved site / Transthyretin signature 2. / Transthyretin, thyroxine binding site / Transthyretin signature 1. / Transthyretin / Transthyretin/hydroxyisourate hydrolase / Transthyretin/hydroxyisourate hydrolase domain / Transthyretin/hydroxyisourate hydrolase domain superfamily / HIUase/Transthyretin family
Similarity search - Domain/homology
Biological speciesMacropus eugenii (tammar wallaby)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsD-Souza, D.G. / Richardson, S.J.
CitationJournal: To Be Published
Title: Structural and amyloidogenic comparisons of human and wallaby transthyretins: implications for amyloidosis?
Authors: D-Souza, D.G. / Richardson, S.J.
History
DepositionJul 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
E: Transthyretin
F: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,70114
Polymers78,1786
Non-polymers5238
Water97354
1
A: Transthyretin
B: Transthyretin
C: Transthyretin
D: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,4459
Polymers52,1184
Non-polymers3275
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
E: Transthyretin
F: Transthyretin
hetero molecules

E: Transthyretin
F: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,51110
Polymers52,1184
Non-polymers3926
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
MethodPISA
Unit cell
Length a, b, c (Å)66.516, 112.152, 245.281
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Components on special symmetry positions
IDModelComponents
11F-311-

HOH

21F-313-

HOH

-
Components

#1: Protein
Transthyretin / Prealbumin


Mass: 13029.587 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macropus eugenii (tammar wallaby) / Gene: TTR / Production host: Escherichia coli (E. coli) / References: UniProt: P42204
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.96 Å3/Da / Density % sol: 58.48 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / Details: 25 mM Tris, 150 mM NaCl pH 8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9984 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 15, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9984 Å / Relative weight: 1
ReflectionResolution: 2.59→46.87 Å / Num. obs: 28992 / % possible obs: 99.8 % / Redundancy: 14.2 % / Biso Wilson estimate: 52.91 Å2 / CC1/2: 0.909 / Rmerge(I) obs: 0.073 / Net I/σ(I): 31.3
Reflection shellResolution: 2.59→2.71 Å / Rmerge(I) obs: 0.585 / Num. unique obs: 3451 / CC1/2: 0.952

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3U2I

3u2i


Resolution: 2.69→37.24 Å / SU ML: 0.3219 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.3925
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 1259 4.84 %RANDOM
Rwork0.1876 24740 --
obs0.1891 25999 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 56.53 Å2
Refinement stepCycle: LAST / Resolution: 2.69→37.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 8 54 5489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01675574
X-RAY DIFFRACTIONf_angle_d1.75867592
X-RAY DIFFRACTIONf_chiral_restr0.1134855
X-RAY DIFFRACTIONf_plane_restr0.0082969
X-RAY DIFFRACTIONf_dihedral_angle_d16.40441935
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.69-2.80.29221210.24162743X-RAY DIFFRACTION100
2.8-2.920.29641490.24912678X-RAY DIFFRACTION100
2.92-3.080.27061600.24852694X-RAY DIFFRACTION100
3.08-3.270.26761330.23742729X-RAY DIFFRACTION100
3.27-3.520.27021360.20752718X-RAY DIFFRACTION100
3.52-3.880.19931620.18022716X-RAY DIFFRACTION100
3.88-4.440.19761350.15932759X-RAY DIFFRACTION99.97
4.44-5.590.15441320.13892791X-RAY DIFFRACTION100
5.59-37.240.20051310.19072912X-RAY DIFFRACTION99.93
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)
14.23773684798-0.9603301211261.873620359591.827554290260.5161281545553.84159380403-0.244424882699-0.2150529028840.9509113880110.0516592156144-0.07456096356210.070452786731-0.763169742524-0.520555490024-1.052392816260.3716650389490.0728646945279-0.01271988000150.191526340592-0.06040155213120.5117094947874.0653.919-46.149
24.50940544752-1.129270335191.6774602292.14012078495-0.1160120900833.733162030060.116518434152-0.374724061423-0.1720830499840.011028647424-0.165953477290.2777511785050.534816739455-0.938611943359-1.36455728338E-90.265679871014-0.1466143724170.03202092625290.4311557262910.006615305277050.29840494725-4.894-13.861-42.803
35.18205887281-0.245898381570.6376131205651.86724906344-0.5339361139154.07347371759-0.0308061927082-0.1476596141330.582637307430.118679820866-0.0918415419972-0.319821455731-0.2658352235840.726562353528-1.41734304255E-90.280766234015-0.0741690295364-0.03335277458160.366201968646-0.02490211957880.38564547920326.417-5.66-35.321
43.275034583260.69281696639-0.006784826027962.56196748208-1.239159920874.283738786710.192066436607-0.12920378568-0.6699920894620.166208198064-0.147233751279-0.3797545136130.9310120256610.322541539232-1.36289629295E-80.5159926788270.0755058363394-0.08085426130510.147621352290.04607776946070.34797622078919.093-24.563-37.836
53.51438474605-0.3621528171140.4507796293952.8129158726-0.871605215925.58041325954-0.1948024997490.02054107674450.56967427314-0.2073541262980.248804133830.165501783584-1.18039800810.4708403821641.49944562048E-90.477253328096-0.218165679867-0.1102736952980.2945192237370.1725891419080.38003314606743.59713.986-8.935
62.79015803541-0.902583524137-0.895482356211.41908117380.2188769439537.59875286339-0.2471909816420.511590052267-0.348466853537-0.2533813928410.07939553655930.1081396317520.4592736588080.2960157743997.88633840893E-90.276305475402-0.1040266899320.01244563432230.3758622473660.003251702105780.26803925903840.395-4.945-15.792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:124 )A10 - 124
2X-RAY DIFFRACTION2( CHAIN B AND RESID 10:124 )B10 - 124
3X-RAY DIFFRACTION3( CHAIN C AND RESID 10:124 )C10 - 124
4X-RAY DIFFRACTION4( CHAIN D AND RESID 10:126 )D10 - 126
5X-RAY DIFFRACTION5( CHAIN E AND RESID 10:124 )E10 - 124
6X-RAY DIFFRACTION6( CHAIN F AND RESID 10:124 )F10 - 124

+
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