[English] 日本語
Yorodumi
- PDB-1ttb: THE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYR... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1ttb
TitleTHE X-RAY CRYSTAL STRUCTURE REFINEMENTS OF NORMAL HUMAN TRANSTHYRETIN AND THE AMYLOIDOGENIC VAL30MET VARIANT TO 1.7 ANGSTROMS RESOLUTION
ComponentsTRANSTHYRETIN
KeywordsTRANSPORT(THYROXINE)
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity ...Defective visual phototransduction due to STRA6 loss of function / negative regulation of glomerular filtration / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / molecular sequestering activity / phototransduction, visible light / Non-integrin membrane-ECM interactions / retinoid metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsSteinrauf, L.K. / Hamilton, J.A. / Braden, B.C.
CitationJournal: J.Biol.Chem. / Year: 1993
Title: The x-ray crystal structure refinements of normal human transthyretin and the amyloidogenic Val-30-->Met variant to 1.7-A resolution.
Authors: Hamilton, J.A. / Steinrauf, L.K. / Braden, B.C. / Liepnieks, J. / Benson, M.D. / Holmgren, G. / Sandgren, O. / Steen, L.
History
DepositionNov 2, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 29, 2017Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)27,6152
Polymers27,6152
Non-polymers00
Water3,153175
1
A: TRANSTHYRETIN
B: TRANSTHYRETIN

A: TRANSTHYRETIN
B: TRANSTHYRETIN


Theoretical massNumber of molelcules
Total (without water)55,2304
Polymers55,2304
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area6380 Å2
ΔGint-45 kcal/mol
Surface area21160 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)43.720, 86.090, 65.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-610-

HOH

21B-618-

HOH

31B-619-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99042, 0.13799, -0.00439), (0.138, 0.99043, -0.00262), (0.00399, -0.00321, -0.99999)
Vector: 37.60101, -2.39622, 98.62653)
DetailsMONOMERS A AND B OF THE DIMER ARE RELATED TO EACH OTHER BY A PSEUDO TWO-FOLD AXIS APPROXIMATELY PARALLEL TO THE CRYSTALLOGRAPHIC 'B' DIRECTION, PERPENDICULAR TO THE SURFACE OF THE SHEETS, AND PASSING BETWEEN THE H STRAND OF ONE MONOMER AND THE H STRAND OF THE OTHER. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *B* WHEN APPLIED TO CHAIN *A*. TWO AB DIMERS ARE ROTATED AROUND THE TWO-FOLD CRYSTALLOGRAPHIC AXIS TO FORM THE TETRAMER, AB-A'B'.

-
Components

#1: Protein TRANSTHYRETIN


Mass: 13807.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P02766
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal grow
*PLUS
Temperature: 22 ℃ / pH: 5.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
238 %ammonium sulfate1reservoir
3100 mMsodium citrate1reservoir

-
Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→5 Å / Rfactor obs: 0.157 / σ(F): 2
Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC ...Details: OCCUPANCIES OF SOLVENT WATER MOLECULES WERE REFINED WITH PROLSQ. OCCUPANCIES OF DISORDERED SIDE CHAINS OR OF ATOMS WITH LESS THAN UNIT OCCUPANCIES WERE SELECTED TO FLATTEN THE FINAL FO-FC DIFFERENCE FOURIER. ATOMS WITH OCCUPANCIES OF 0.00 HAVE NO OBSERVABLE ELECTRON DENSITY. SHEET IDENTIFIERS ARE BASED ON PROTEIN DATA BANK ENTRY 2PAB (PREALBUMIN, OATLEY AND BLAKE).
Refinement stepCycle: LAST / Resolution: 1.7→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1948 0 0 175 2123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.5
Software
*PLUS
Name: 'PROTIN and PROLSQ' / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18320
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal targetDev ideal
X-RAY DIFFRACTIONp_bond_d0.03
X-RAY DIFFRACTIONp_angle_d0.040.029
X-RAY DIFFRACTIONp_plane_restr0.020.005
X-RAY DIFFRACTIONp_mcbond_it10.668
X-RAY DIFFRACTIONp_scbond_it1.50.914
X-RAY DIFFRACTIONp_mcangle_it1.51.186
X-RAY DIFFRACTIONp_scangle_it21.444

+
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