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- PDB-6igg: Crystal structure of FT condition 1 -

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Basic information

Entry
Database: PDB / ID: 6igg
TitleCrystal structure of FT condition 1
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 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 1.1Mar 25, 2020Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details
Revision 1.2Nov 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

Downloads & links

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Assembly

Deposited unit
A: Protein FLOWERING LOCUS T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9309
Polymers19,4341
Non-polymers4978
Water4,306239
1
A: Protein FLOWERING LOCUS T
hetero molecules

A: Protein FLOWERING LOCUS T
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,86118
Polymers38,8682
Non-polymers99316
Water362
TypeNameSymmetry operationNumber
crystal symmetry operation2_565-x+1/2,-y+1,z+1/21
crystal symmetry operation4_556x+1/2,-y+1/2,-z+11
Unit cell
Length a, b, c (Å)39.618, 48.715, 73.571
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 1-167 / 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.: 8 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 1.83 Å3/Da / Density % sol: 32.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PEG1500, MPD, and 0.1 M Tris-HCl, pH 8.5

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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→50 Å / Num. obs: 75289 / % possible obs: 97.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 5.9 Å2 / CC1/2: 0.998 / Net I/σ(I): 11.9
Reflection shellResolution: 1→1.02 Å / Mean I/σ(I) obs: 1.2 / Num. unique obs: 3370 / CC1/2: 0.655

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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→30.74 Å / SU ML: 0.0601 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 10.9446
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1356 3711 4.93 %
Rwork0.1163 71578 -
obs0.1172 75289 97.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 9.25 Å2
Refinement stepCycle: LAST / Resolution: 1→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1364 0 32 239 1635
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01321508
X-RAY DIFFRACTIONf_angle_d1.33182055
X-RAY DIFFRACTIONf_chiral_restr0.1095225
X-RAY DIFFRACTIONf_plane_restr0.0115272
X-RAY DIFFRACTIONf_dihedral_angle_d3.3799871
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1-1.010.2727670.27321485X-RAY DIFFRACTION54.3
1.01-1.030.22591090.25152232X-RAY DIFFRACTION82.78
1.03-1.040.23071440.21662502X-RAY DIFFRACTION93.1
1.04-1.060.2121360.18422558X-RAY DIFFRACTION96.08
1.06-1.070.16361370.15962675X-RAY DIFFRACTION97.64
1.07-1.090.15391280.13852655X-RAY DIFFRACTION98.03
1.09-1.110.1411320.12812678X-RAY DIFFRACTION99.08
1.11-1.120.11751380.11572662X-RAY DIFFRACTION99.68
1.12-1.150.15551470.11172710X-RAY DIFFRACTION99.79
1.15-1.170.11311380.11022710X-RAY DIFFRACTION99.82
1.17-1.190.13661300.11122710X-RAY DIFFRACTION100
1.19-1.220.13371450.10792676X-RAY DIFFRACTION99.96
1.22-1.250.11661620.10332722X-RAY DIFFRACTION99.97
1.25-1.280.11871550.10052699X-RAY DIFFRACTION100
1.28-1.310.1361340.09962729X-RAY DIFFRACTION100
1.31-1.350.11361460.09782697X-RAY DIFFRACTION100
1.35-1.390.12431390.09742722X-RAY DIFFRACTION99.93
1.39-1.440.12421480.0932723X-RAY DIFFRACTION100
1.44-1.50.11571420.08972723X-RAY DIFFRACTION99.93
1.5-1.570.12171500.08762733X-RAY DIFFRACTION100
1.57-1.650.10621380.0892741X-RAY DIFFRACTION100
1.65-1.750.11981430.09522738X-RAY DIFFRACTION100
1.75-1.890.11251620.09822751X-RAY DIFFRACTION100
1.89-2.080.11131380.09472762X-RAY DIFFRACTION100
2.08-2.380.12321340.10482791X-RAY DIFFRACTION100
2.38-30.13731430.12342821X-RAY DIFFRACTION100
3-30.740.16741260.13712973X-RAY DIFFRACTION99.81

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