[English] 日本語
Yorodumi
- PDB-6igh: Crystal structure of FT condition3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6igh
TitleCrystal structure of FT condition3
ComponentsProtein FLOWERING LOCUS T
KeywordsPLANT PROTEIN / flowering control
Function / homology
Function and homology information


meristem determinacy / photoperiodism, flowering / positive regulation of flower development / regulation of flower development / regulation of stomatal movement / flower development / phosphatidylethanolamine binding / cell differentiation / endoplasmic reticulum / nucleus / cytoplasm
Similarity search - Function
Phosphatidylethanolamine-binding, conserved site / Phosphatidylethanolamine-binding protein family signature. / Phosphatidylethanolamine-binding Protein / PEBP-like / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Protein FLOWERING LOCUS T
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.01 Å
AuthorsWatanabe, S. / Nakamura, Y. / Kanehara, K. / Inaba, K.
CitationJournal: Iscience / Year: 2019
Title: High-Resolution Crystal Structure of Arabidopsis FLOWERING LOCUS T Illuminates Its Phospholipid-Binding Site in Flowering.
Authors: Nakamura, Y. / Lin, Y.C. / Watanabe, S. / Liu, Y.C. / Katsuyama, K. / Kanehara, K. / Inaba, K.
History
DepositionSep 25, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein FLOWERING LOCUS T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6825
Polymers19,4341
Non-polymers2484
Water5,296294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area730 Å2
ΔGint11 kcal/mol
Surface area8800 Å2
Unit cell
Length a, b, c (Å)48.889, 60.956, 63.799
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

-
Components

#1: Protein Protein FLOWERING LOCUS T


Mass: 19433.900 Da / Num. of mol.: 1 / Fragment: UNP residues 1-168 / Mutation: C107S, C164S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FT / Production host: Escherichia coli (E. coli) / References: UniProt: Q9SXZ2
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.46 Å3/Da / Density % sol: 49.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG4000 and ammonium citrate/citric acid, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.01→50 Å / Num. obs: 97694 / % possible obs: 97.4 % / Redundancy: 7.4 % / Biso Wilson estimate: 9.15 Å2 / CC1/2: 0.994 / Net I/σ(I): 9.8
Reflection shellResolution: 1.01→1.03 Å / Num. unique obs: 6267 / CC1/2: 0.833

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKP

1wkp


Resolution: 1.01→32.74 Å / SU ML: 0.0671 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.5215
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1385 4869 4.98 %
Rwork0.1169 92824 -
obs0.1179 97693 97.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.64 Å2
Refinement stepCycle: LAST / Resolution: 1.01→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1343 0 16 294 1653
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01451498
X-RAY DIFFRACTIONf_angle_d1.47282052
X-RAY DIFFRACTIONf_chiral_restr0.1198223
X-RAY DIFFRACTIONf_plane_restr0.0121279
X-RAY DIFFRACTIONf_dihedral_angle_d3.4067852
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.01-1.020.22531630.18172936X-RAY DIFFRACTION93.63
1.02-1.030.18131620.16783007X-RAY DIFFRACTION95.42
1.03-1.050.16811520.15372978X-RAY DIFFRACTION94.93
1.05-1.060.15831610.14133007X-RAY DIFFRACTION95.45
1.06-1.070.16311340.13413015X-RAY DIFFRACTION95.34
1.07-1.090.14841700.13053001X-RAY DIFFRACTION95.51
1.09-1.10.12651680.12082985X-RAY DIFFRACTION95.89
1.1-1.120.13481630.10863023X-RAY DIFFRACTION96.22
1.12-1.140.13361520.1083006X-RAY DIFFRACTION95.49
1.14-1.160.1231680.10423049X-RAY DIFFRACTION96.87
1.16-1.180.13141630.10263047X-RAY DIFFRACTION96.51
1.18-1.20.11571800.09943030X-RAY DIFFRACTION96.45
1.2-1.220.12861700.10083058X-RAY DIFFRACTION97.08
1.22-1.250.12841520.09963065X-RAY DIFFRACTION97.13
1.25-1.270.12491620.13047X-RAY DIFFRACTION97.15
1.27-1.30.14261690.09823094X-RAY DIFFRACTION97.55
1.3-1.340.12511490.10023083X-RAY DIFFRACTION97.76
1.34-1.370.12211460.0973116X-RAY DIFFRACTION97.84
1.37-1.410.111620.09543110X-RAY DIFFRACTION98.05
1.41-1.460.12271520.09413142X-RAY DIFFRACTION98.21
1.46-1.510.1151780.09483101X-RAY DIFFRACTION98.44
1.51-1.570.10571700.09523119X-RAY DIFFRACTION98.27
1.57-1.640.10911770.09723141X-RAY DIFFRACTION98.69
1.64-1.730.1311690.09993145X-RAY DIFFRACTION99.31
1.73-1.840.12051600.10553186X-RAY DIFFRACTION98.94
1.84-1.980.12811620.10513184X-RAY DIFFRACTION99.35
1.98-2.180.12491550.10813232X-RAY DIFFRACTION99.65
2.18-2.490.14551890.11813204X-RAY DIFFRACTION99.71
2.49-3.140.15731670.13273281X-RAY DIFFRACTION99.83
3.14-32.740.16751440.14543432X-RAY DIFFRACTION99.28

+
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