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- PDB-6igj: Crystal structure of FT condition 4 -

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Basic information

Entry
Database: PDB / ID: 6igj
TitleCrystal structure of FT condition 4
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: 1.501 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_symmetry

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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)19,4582
Polymers19,4341
Non-polymers241
Water2,594144
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area90 Å2
ΔGint-6 kcal/mol
Surface area8780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.503, 53.503, 103.975
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O

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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: 2.22 Å3/Da / Density % sol: 44.61 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NaCl, PEG3350, MgCl2, imidazole-HCl

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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: Nov 19, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 28282 / % possible obs: 99.9 % / Redundancy: 10.5 % / CC1/2: 0.999 / Net I/σ(I): 14.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 1734 / CC1/2: 0.709

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WKP

1wkp


Resolution: 1.501→42.323 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.09
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2249 1333 4.72 %
Rwork0.1969 --
obs0.1983 28242 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.501→42.323 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1327 0 1 144 1472
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091378
X-RAY DIFFRACTIONf_angle_d0.991886
X-RAY DIFFRACTIONf_dihedral_angle_d12.558825
X-RAY DIFFRACTIONf_chiral_restr0.066212
X-RAY DIFFRACTIONf_plane_restr0.008251
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.501-1.55450.29771250.27982656X-RAY DIFFRACTION100
1.5545-1.61670.32081740.26532582X-RAY DIFFRACTION100
1.6167-1.69030.28841230.25192665X-RAY DIFFRACTION100
1.6903-1.77940.25521400.23832654X-RAY DIFFRACTION100
1.7794-1.89090.23771310.22062682X-RAY DIFFRACTION100
1.8909-2.03690.22051060.19882680X-RAY DIFFRACTION100
2.0369-2.24190.24171210.1952712X-RAY DIFFRACTION100
2.2419-2.56630.21451230.19522702X-RAY DIFFRACTION100
2.5663-3.2330.20581320.20142734X-RAY DIFFRACTION100
3.233-42.3230.21461580.17512842X-RAY DIFFRACTION99

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