[English] 日本語
Yorodumi
- PDB-4ikj: Crystal structure of wild-type human transthyretin in complex wit... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4ikj
TitleCrystal structure of wild-type human transthyretin in complex with sulindac
ComponentsTransthyretin
KeywordsTRANSPORT PROTEIN / Hormone carrier / Retinol binding protein
Function / homology
Function and homology information


Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen ...Defective visual phototransduction due to STRA6 loss of function / The canonical retinoid cycle in rods (twilight vision) / purine nucleobase metabolic process / hormone binding / Non-integrin membrane-ECM interactions / molecular sequestering activity / Retinoid metabolism and transport / retinoid metabolic process / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / protein-containing complex binding / protein-containing complex / : / 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
Chem-SUZ / Transthyretin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLima, L.M.T.R.
CitationJournal: To be Published
Title: Crystal structure of wild-type human transthyretin in complex with sulindac
Authors: Lima, L.M.T.R.
History
DepositionDec 26, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 30, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2684
Polymers27,5552
Non-polymers7132
Water2,792155
1
A: Transthyretin
B: Transthyretin
hetero molecules

A: Transthyretin
B: Transthyretin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,5358
Polymers55,1094
Non-polymers1,4264
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area6070 Å2
ΔGint-43 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.420, 83.490, 63.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

-
Components

#1: Protein Transthyretin / ATTR / Prealbumin / TBPA


Mass: 13777.360 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766
#2: Chemical ChemComp-SUZ / [(1Z)-5-fluoro-2-methyl-1-{4-[methylsulfinyl]benzylidene}-1H-inden-3-yl]acetic acid / SULINDAC


Mass: 356.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H17FO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.05 Å3/Da / Density % sol: 40.07 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10mg/mL wtTTR, 0.2M Calcium chloride, 0.1M HEPES sodium pH 7.5, 28% v/v Polyethylene glycol 400 (Hampton Research's Crystal Screen I, #14), VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.425 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.425 Å / Relative weight: 1
ReflectionResolution: 2.1→63.888 Å / Num. all: 13202 / Num. obs: 13202 / % possible obs: 95.9 % / Redundancy: 3 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Net I/σ(I): 12
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.1-2.212.90.280.2313.1581319740.1560.280.2314.499.8
2.21-2.3530.2410.1993.7566318630.1330.2410.1994.999.8
2.35-2.513.10.1980.1644.2536417230.1090.1980.1646.898.3
2.51-2.713.10.1630.1365496115980.0890.1630.1369.397.3
2.71-2.973.10.1050.0877.9450514310.0570.1050.08712.694
2.97-3.323.10.080.0679.9390712760.0440.080.06716.591.8
3.32-3.833.10.0680.05610.8333010900.0370.0680.05621.888.7
3.83-4.72.90.0560.04612.127869510.0310.0560.04623.890.5
4.7-6.642.80.050.04113.423318260.0270.050.0412297.7
6.64-19.8422.90.0480.03812.913474700.0280.0480.03822.294.5

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.17 Å19.84 Å
Translation2.17 Å19.84 Å

-
Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.2.25data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.84 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.9 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.1798 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8295 / SU B: 5.949 / SU ML: 0.157 / SU R Cruickshank DPI: 0.2884 / SU Rfree: 0.2243 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.31 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2572 777 5.9 %RANDOM
Rwork0.1981 ---
obs0.2014 13182 95.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 71.22 Å2 / Biso mean: 24.1206 Å2 / Biso min: 9.21 Å2
Baniso -1Baniso -2Baniso -3
1-3.75 Å20 Å20 Å2
2---2.87 Å20 Å2
3----0.88 Å2
Refinement stepCycle: LAST / Resolution: 2.1→19.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1785 0 50 155 1990
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221998
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9732746
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8745253
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.95323.97683
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.315304
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.927159
X-RAY DIFFRACTIONr_chiral_restr0.0780.2300
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211567
X-RAY DIFFRACTIONr_mcbond_it0.6831.51224
X-RAY DIFFRACTIONr_mcangle_it1.27622002
X-RAY DIFFRACTIONr_scbond_it1.723774
X-RAY DIFFRACTIONr_scangle_it2.7294.5744
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 55 -
Rwork0.222 938 -
all-993 -
obs--99.6 %

+
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