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- PDB-6igi: Crystal structure of FT condition 2 -

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Basic information

Entry
Database: PDB / ID: 6igi
TitleCrystal structure of FT condition 2
ComponentsProtein FLOWERING LOCUS T
KeywordsPLANT PROTEIN / flowering control
Function / homology
Function and homology information


meristem determinacy / photoperiodism, flowering / regulation of flower development / positive regulation of flower development / flower development / regulation of stomatal movement / 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: 1.33 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein FLOWERING LOCUS T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4962
Polymers19,4341
Non-polymers621
Water3,621201
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint3 kcal/mol
Surface area8150 Å2
Unit cell
Length a, b, c (Å)48.482, 51.537, 56.908
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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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.: 1 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: isopropanol,PEG3350 and ammonium citrate/citric acid

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.33→50 Å / Num. obs: 33436 / % possible obs: 99.9 % / Redundancy: 6.4 % / Biso Wilson estimate: 12.22 Å2 / CC1/2: 0.999 / Net I/σ(I): 12.9
Reflection shellResolution: 1.33→1.36 Å / Num. unique obs: 2167 / CC1/2: 0.56

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Processing

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

1wkp


Resolution: 1.33→30.01 Å / SU ML: 0.1311 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.1253
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1864 1634 4.89 %
Rwork0.1597 31794 -
obs0.1609 33428 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.02 Å2
Refinement stepCycle: LAST / Resolution: 1.33→30.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1297 0 4 201 1502
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01091394
X-RAY DIFFRACTIONf_angle_d1.16951913
X-RAY DIFFRACTIONf_chiral_restr0.0952210
X-RAY DIFFRACTIONf_plane_restr0.0086259
X-RAY DIFFRACTIONf_dihedral_angle_d3.0942813
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.370.31861250.2622568X-RAY DIFFRACTION98.39
1.37-1.410.27491500.24672602X-RAY DIFFRACTION99.89
1.41-1.460.26521400.2322615X-RAY DIFFRACTION100
1.46-1.520.20971350.20872626X-RAY DIFFRACTION99.96
1.52-1.590.2171430.18342611X-RAY DIFFRACTION100
1.59-1.670.16631390.16492634X-RAY DIFFRACTION100
1.67-1.780.15321260.15342641X-RAY DIFFRACTION99.93
1.78-1.920.20371280.14552643X-RAY DIFFRACTION100
1.92-2.110.14811490.13712643X-RAY DIFFRACTION100
2.11-2.420.16721520.13342649X-RAY DIFFRACTION99.96
2.42-3.040.17561300.14672720X-RAY DIFFRACTION99.89
3.04-30.010.18541170.15412842X-RAY DIFFRACTION99.66
Refinement TLS params.Method: refined / Origin x: -11.2860822745 Å / Origin y: -10.4139689244 Å / Origin z: 10.7855244797 Å
111213212223313233
T0.0736987008343 Å20.00184222908425 Å2-0.0116319482348 Å2-0.0653071673469 Å2-0.015430153171 Å2--0.0806757072338 Å2
L1.31153178632 °20.153225099981 °2-0.175201371577 °2-0.879073662888 °20.247071813968 °2--1.23597672939 °2
S0.0220417494469 Å °-0.0102550723833 Å °-0.135748349776 Å °0.0294477571539 Å °0.0225353917504 Å °-0.123588442591 Å °0.0390154410114 Å °0.091450559324 Å °-0.0254322044877 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 7 through 168)

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