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- PDB-6igh: Crystal structure of FT condition3 -

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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 / 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 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / 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

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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)19,6825
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

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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.: 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

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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: 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

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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

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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: 1.01→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

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