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- PDB-1wko: Terminal flower 1 (tfl1) from arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 1wko
TitleTerminal flower 1 (tfl1) from arabidopsis thaliana
ComponentsTERMINAL FLOWER 1 protein
KeywordsSIGNALING PROTEIN / cis-peptide / pebp
Function / homology
Function and homology information


: / meristem determinacy / negative regulation of flower development / vegetative to reproductive phase transition of meristem / flower development / response to sucrose / protein targeting to vacuole / vacuole / transcription coregulator activity / vesicle ...: / meristem determinacy / negative regulation of flower development / vegetative to reproductive phase transition of meristem / flower development / response to sucrose / protein targeting to vacuole / vacuole / transcription coregulator activity / vesicle / cell differentiation / nucleus / plasma membrane / 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 TERMINAL FLOWER 1
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiller, D. / Banfield, M.J. / Winter, V.J. / Brady, R.L.
CitationJournal: Embo J. / Year: 2006
Title: A divergent external loop confers antagonistic activity on floral regulators FT and TFL1.
Authors: Ahn, J.H. / Miller, D. / Winter, V.J. / Banfield, M.J. / Lee, J.H. / Yoo, S.Y. / Henz, S.R. / Brady, R.L. / Weigel, D.
History
DepositionJun 1, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 25, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TERMINAL FLOWER 1 protein
B: TERMINAL FLOWER 1 protein


Theoretical massNumber of molelcules
Total (without water)40,9392
Polymers40,9392
Non-polymers00
Water7,188399
1
A: TERMINAL FLOWER 1 protein


Theoretical massNumber of molelcules
Total (without water)20,4701
Polymers20,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TERMINAL FLOWER 1 protein


Theoretical massNumber of molelcules
Total (without water)20,4701
Polymers20,4701
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.347, 109.347, 64.697
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-354-

HOH

21B-355-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
151A
161B
171A
181B
191A
201B
211A
221B
231A
241B
251A
261B
271A
281B
12A
22B
13A
23B
14A
24B
15A
25B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALGLYGLY6AA8 - 1511 - 18
211VALVALGLYGLY6BB8 - 1511 - 18
321PHEPHELEULEU6AA146 - 159149 - 162
421PHEPHELEULEU6BB146 - 159149 - 162
531LYSLYSILEILE6AA54 - 5957 - 62
631LYSLYSILEILE6BB54 - 5957 - 62
741ALAALAGLUGLU6AA168 - 171171 - 174
841ALAALAGLUGLU6BB168 - 171171 - 174
951LEULEUASNASN5AA85 - 9588 - 98
1051LEULEUASNASN5BB85 - 9588 - 98
1161ASPASPPHEPHE4AA82 - 8485 - 87
1261ASPASPPHEPHE4BB82 - 8485 - 87
1371ILEILEILEILE6AA96 - 12099 - 123
1471ILEILEILEILE6BB96 - 12099 - 123
1581HISHISPHEPHE1AA121 - 128124 - 131
1681HISHISPHEPHE1BB121 - 128124 - 131
1791PROPROASNASN5AA160 - 167163 - 170
1891PROPROASNASN5BB160 - 167163 - 170
19101ASPASPPROPRO5AA76 - 8079 - 83
20101ASPASPPROPRO5BB76 - 8079 - 83
21111PHEPHELEULEU4AA68 - 7071 - 73
22111PHEPHELEULEU4BB68 - 7071 - 73
23121THRTHRVALVAL4AA29 - 4032 - 43
24121THRTHRVALVAL4BB29 - 4032 - 43
25131VALVALPHEPHE4AA17 - 2420 - 27
26131VALVALPHEPHE4BB17 - 2420 - 27
27141METMETPROPRO4AA72 - 7575 - 78
28141METMETPROPRO4BB72 - 7575 - 78
112PHEPHESERSER5AA47 - 4950 - 52
212PHEPHESERSER5BB47 - 4950 - 52
113ILEILEILEILE6AA136 - 140139 - 143
213ILEILEILEILE6BB136 - 140139 - 143
114SERSERGLYGLY6AA41 - 4344 - 46
214SERSERGLYGLY6BB41 - 4344 - 46
115PHEPHETHRTHR1AA25 - 2828 - 31
215PHEPHETHRTHR1BB25 - 2828 - 31

NCS ensembles :
ID
1
2
3
4
5
Detailsmonomer is the biological unit

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Components

#1: Protein TERMINAL FLOWER 1 protein


Mass: 20469.510 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: TFL1 / Plasmid: pet-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21 (de3) / References: UniProt: P93003
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.3M (NH4)2SO4, 22% w/v PEG 5000 MME, 0.1M cacodylate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 12, 2001 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 41659 / % possible obs: 100 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 20.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1qou

1qou


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.952 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.114 / ESU R Free: 0.106 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20672 2074 5 %RANDOM
Rwork0.1844 ---
obs0.1855 39517 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 20.238 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.16 Å20 Å2
2--0.31 Å20 Å2
3----0.47 Å2
Refinement stepCycle: LAST / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2649 0 0 399 3048
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222763
X-RAY DIFFRACTIONr_angle_refined_deg1.5391.9433747
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515328
X-RAY DIFFRACTIONr_chiral_restr0.1110.2409
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022122
X-RAY DIFFRACTIONr_nbd_refined0.1950.21204
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2292
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.227
X-RAY DIFFRACTIONr_mcbond_it0.8341.51657
X-RAY DIFFRACTIONr_mcangle_it1.36522733
X-RAY DIFFRACTIONr_scbond_it1.93531106
X-RAY DIFFRACTIONr_scangle_it3.0744.51014
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
176tight positional0.360.05
532tight positional0.060.05
1334medium positional0.170.5
212medium positional0.050.5
1529loose positional0.365
212loose positional0.275
342loose positional0.345
418loose positional0.125
176tight thermal0.240.5
532tight thermal0.350.5
1334medium thermal0.742
212medium thermal3.272
1529loose thermal1.4910
212loose thermal3.0810
342loose thermal3.410
418loose thermal0.3310
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.258 147
Rwork0.197 2896
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9572-0.048-0.41161.57950.77863.9186-0.01680.0809-0.026-0.08230.00160.06210.2644-0.36640.01530.0725-0.0451-0.02480.0437-0.0040.0562-21.331382.402119.6178
21.3080.5926-0.05463.88510.85051.55510.0165-0.08920.10910.2991-0.1030.61960.0742-0.18980.08650.0437-0.03430.04520.065-0.00940.0952-18.859859.8062-14.4779
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA8 - 17111 - 174
2X-RAY DIFFRACTION2BB8 - 17111 - 174

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