[English] 日本語
Yorodumi
- PDB-1kgi: Rat transthyretin (also called prealbumin) complex with 3,3',5,5'... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kgi
TitleRat transthyretin (also called prealbumin) complex with 3,3',5,5'-tetraiodothyroacetic acid (t4ac)
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT PROTEIN / PREALBUMIN / TRANSPORT / TETRAIODOTHYROACETIC ACID / THYROID HO
Function / homology
Function and homology information


The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex ...The canonical retinoid cycle in rods (twilight vision) / Retinoid metabolism and transport / thyroid hormone metabolic process / hormone binding / Neutrophil degranulation / thyroid hormone binding / purine nucleobase metabolic process / hormone activity / protein-containing complex binding / protein-containing complex / extracellular space / identical protein binding
Similarity search - Function
Transthyretin/hydroxyisourate hydrolase domain / 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 ...Transthyretin/hydroxyisourate hydrolase domain / 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 / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
3,3',5,5'-TETRAIODOTHYROACETIC ACID / Transthyretin
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsWojtczak, A. / Neumann, P. / Muziol, T. / Cody, V. / Luft, J.R. / Pangborn, W.
Citation
Journal: Acta Biochim.Pol. / Year: 2001
Title: Complex of rat transthyretin with tetraiodothyroacetic acid refined at 2.1 and 1.8 A resolution.
Authors: Muziol, T. / Cody, V. / Luft, J.R. / Pangborn, W. / Wojtczak, A.
#1: Journal: J.Biol.Chem. / Year: 1993
Title: Structural Aspects of Inotropic Bipyridine Binding. Crystal Structure Determination to 1.9 A of the Human Serum Transthyretin-Milrinone Complex
Authors: Wojtczak, A. / Luft, J.R. / Cody, V.
#2: Journal: J.Biol.Chem. / Year: 1992
Title: Mechanism of Molecular Recognition. Structural Aspects of 3,3'-Diiodo-L-Thyronine Binding to Human Serum Transthyretin
Authors: Wojtczak, A. / Luft, J. / Cody, V.
#3: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structures of Human Transthyretin Complexed with Thyroxine at 2.0 A Resolution and 3',5'-Dinitro-N-Acetyl-L-Thyronine at 2.2 A Resolution
Authors: Wojtczak, A. / Cody, V. / Luft, J.R. / Pangborn, W.
#4: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of New Polymorphic Monoclinic Form of Hum Transthyretin at 3A Resolution Reveals a Mixed Comp between Unliganded and T4-Bound Tetramers of Ttr
Authors: Wojtczak, A. / Neumann, P. / Cody, V.
#5: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: STRUCTURE OF RAT (rTTR) TRANSTHYRETIN COMPLEX WITH THYROXINE AT 2.5 A RESOLUTION: FIRST NON-BIASED INS INTO THYROXINE BINDING REVEALS DIFFERENT HORMONE ORIENTATION IN TWO BINDING SITES
Authors: Wojtczak, A. / Cody, V. / Luft, J. / Pangborn, W.
History
DepositionNov 27, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Refinement description / Category: diffrn_source / software / Item: _diffrn_source.type
Revision 1.4Aug 16, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN
C: TRANSTHYRETIN
D: TRANSTHYRETIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,9526
Polymers54,4574
Non-polymers1,4962
Water5,062281
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8140 Å2
ΔGint-37 kcal/mol
Surface area20050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.510, 81.510, 160.238
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein
TRANSTHYRETIN / Prealbumin / TBPA


Mass: 13614.147 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Tissue: plasma / References: UniProt: P02767
#2: Chemical ChemComp-T4A / 3,3',5,5'-TETRAIODOTHYROACETIC ACID


Mass: 747.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H8I4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 281 / 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: 2.38 Å3/Da / Density % sol: 46.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: ammonium sulphate, acetate buffer,, pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Type: CHESS / Wavelength: 0.9109 / Wavelength: 0.9109 Å
DetectorType: HAMLIN/UCSD / Detector: IMAGE PLATE / Date: Feb 1, 1997 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9109 Å / Relative weight: 1
ReflectionResolution: 1.8→46.787 Å / Num. all: 35710 / Num. obs: 35710 / % possible obs: 70.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.31 % / Biso Wilson estimate: 20.6 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 24.7
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 5.15 % / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 2.3 / Num. unique all: 884 / % possible all: 28
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 46.7 Å
Reflection shell
*PLUS
% possible obs: 28 %

-
Processing

Software
NameVersionClassification
HAMLIN/UCSDdata collection
HAMLIN/UCSDdata reduction
CNS1.1refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
CNS1.1phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: TETRAMER OF RAT TTR, PDB ENTRY 1GKE

1gke


Resolution: 1.8→8 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 701266.33 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood
RfactorNum. reflection% reflectionSelection details
Rfree0.24 2620 8.1 %RANDOM
Rwork0.207 ---
all0.21 35710 --
obs0.204 32345 64.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.616 Å2 / ksol: 0.41342 e/Å3
Displacement parametersBiso mean: 33.5 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å20 Å20 Å2
2--2.47 Å20 Å2
3----4.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.8→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3737 0 88 281 4106
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.198
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.05
X-RAY DIFFRACTIONc_mcbond_it2.31.5
X-RAY DIFFRACTIONc_mcangle_it3.742
X-RAY DIFFRACTIONc_scbond_it10.982
X-RAY DIFFRACTIONc_scangle_it10.42.5
LS refinement shellResolution: 1.8→1.84 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.217 36 8.1 %
Rwork0.208 409 -
obs-409 15.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3PARAMETER3C.INPTOPOLOGY3C.INP
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.05

+
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://pdbjlvh1.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