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- PDB-1wkp: Flowering locus t (ft) from arabidopsis thaliana -

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Basic information

Entry
Database: PDB / ID: 1wkp
TitleFlowering locus t (ft) from arabidopsis thaliana
ComponentsFLOWERING LOCUS T protein
KeywordsSIGNALING PROTEIN / cis-peptide / pebp
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: 2.6 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 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FLOWERING LOCUS T protein
B: FLOWERING LOCUS T protein
C: FLOWERING LOCUS T protein
D: FLOWERING LOCUS T protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,7957
Polymers77,5074
Non-polymers2883
Water3,513195
1
A: FLOWERING LOCUS T protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5693
Polymers19,3771
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FLOWERING LOCUS T protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4732
Polymers19,3771
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: FLOWERING LOCUS T protein


Theoretical massNumber of molelcules
Total (without water)19,3771
Polymers19,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: FLOWERING LOCUS T protein


Theoretical massNumber of molelcules
Total (without water)19,3771
Polymers19,3771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
B: FLOWERING LOCUS T protein
C: FLOWERING LOCUS T protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,8503
Polymers38,7542
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1870 Å2
ΔGint-18 kcal/mol
Surface area15520 Å2
MethodPISA
6
A: FLOWERING LOCUS T protein
D: FLOWERING LOCUS T protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9464
Polymers38,7542
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2010 Å2
ΔGint-27 kcal/mol
Surface area15740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.973, 61.542, 66.841
Angle α, β, γ (deg.)75.15, 72.18, 70.55
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51A
61B
71C
81D
91A
101B
111C
121D
131A
141B
151C
161D
171A
181B
191C
201D
211A
221B
231C
241D
251A
261B
271C
281D
291A
301B
311C
321D
331A
341B
351C
361D
371A
381B
391C
401D
411A
421B
431C
441D
451A
461B
471C
481D
491A
501B
511C
521D
531A
541B
551C
561D
571A
581B
591C
601D
12A
22B
32A
42B
52A
62B
72A
82B
92A
102B
13C
23D
33C
43D
53C
63D
73C
83D
14A
24C
34D
15A
25B
35A
45B
16C
26D
36C
46D

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
111ILEILESERSER1AA10 - 1213 - 15
211ILEILESERSER1BB10 - 1213 - 15
311ILEILESERSER1CC10 - 1213 - 15
411ILEILESERSER1DD10 - 1213 - 15
521ARGARGILEILE1AA119 - 123122 - 126
621ARGARGILEILE1BB119 - 123122 - 126
721ARGARGILEILE1CC119 - 123122 - 126
821ARGARGILEILE1DD119 - 123122 - 126
931ASNASNSERSER1AA141 - 164144 - 167
1031ASNASNSERSER1BB141 - 164144 - 167
1131ASNASNSERSER1CC141 - 164144 - 167
1231ASNASNSERSER1DD141 - 164144 - 167
1341VALVALASPASP1AA14 - 2017 - 23
1441VALVALASPASP1BB14 - 2017 - 23
1541VALVALASPASP1CC14 - 2017 - 23
1641VALVALASPASP1DD14 - 2017 - 23
1751SERSERGLUGLU1AA107 - 109110 - 112
1851SERSERGLUGLU1BB107 - 109110 - 112
1951SERSERGLUGLU1CC107 - 109110 - 112
2051SERSERGLUGLU1DD107 - 109110 - 112
2161ARGARGLEULEU6AA6 - 99 - 12
2261ARGARGLEULEU6BB6 - 99 - 12
2361ARGARGLEULEU6CC6 - 99 - 12
2461ARGARGLEULEU6DD6 - 99 - 12
2571PHEPHESERSER1AA64 - 7867 - 81
2671PHEPHESERSER1BB64 - 7867 - 81
2771PHEPHESERSER1CC64 - 7867 - 81
2871PHEPHESERSER1DD64 - 7867 - 81
2981ASPASPGLYGLY1AA92 - 10295 - 105
3081ASPASPGLYGLY1BB92 - 10295 - 105
3181ASPASPGLYGLY1CC92 - 10295 - 105
3281ASPASPGLYGLY1DD92 - 10295 - 105
3391GLNGLNGLUGLU6AA165 - 167168 - 170
3491GLNGLNGLUGLU6BB165 - 167168 - 170
3591GLNGLNGLUGLU6CC165 - 167168 - 170
3691GLNGLNGLUGLU6DD165 - 167168 - 170
37101PROPROLEULEU1AA45 - 6148 - 64
38101PROPROLEULEU1BB45 - 6148 - 64
39101PROPROLEULEU1CC45 - 6148 - 64
40101PROPROLEULEU1DD45 - 6148 - 64
41111THRTHRLEULEU1AA27 - 4330 - 46
42111THRTHRLEULEU1BB27 - 4330 - 46
43111THRTHRLEULEU1CC27 - 4330 - 46
44111THRTHRLEULEU1DD27 - 4330 - 46
45121PROPROLEULEU1AA80 - 8283 - 85
46121PROPROLEULEU1BB80 - 8283 - 85
47121PROPROLEULEU1CC80 - 8283 - 85
48121PROPROLEULEU1DD80 - 8283 - 85
49131GLUGLUVALVAL1AA84 - 9087 - 93
50131GLUGLUVALVAL1BB84 - 9087 - 93
51131GLUGLUVALVAL1CC84 - 9087 - 93
52131GLUGLUVALVAL1DD84 - 9087 - 93
53141SERSERVALVAL3AA12 - 1415 - 17
54141SERSERVALVAL3BB12 - 1415 - 17
55141SERSERVALVAL3CC12 - 1415 - 17
56141SERSERVALVAL3DD12 - 1415 - 17
57151ASNASNSERSER1AA23 - 2526 - 28
58151ASNASNSERSER1BB23 - 2526 - 28
59151ASNASNSERSER1CC23 - 2526 - 28
60151ASNASNSERSER1DD23 - 2526 - 28
112PHEPHEGLYGLY1AA125 - 129128 - 132
212PHEPHEGLYGLY1BB125 - 129128 - 132
322ARGARGARGARG1AA8386
422ARGARGARGARG1BB8386
532ASNASNVALVAL1AA103 - 106106 - 109
632ASNASNVALVAL1BB103 - 106106 - 109
742GLNGLNGLYGLY1AA131 - 137134 - 140
842GLNGLNGLYGLY1BB131 - 137134 - 140
952ARGARGARGARG5AA130133
1052ARGARGARGARG5BB130133
113PHEPHEGLYGLY1CC125 - 137128 - 140
213PHEPHEGLYGLY1DD125 - 137128 - 140
323ARGARGGLNGLN1CC139 - 140142 - 143
423ARGARGGLNGLN1DD139 - 140142 - 143
533ARGARGARGARG1CC8386
633ARGARGARGARG1DD8386
743ASNASNILEILE2CC103 - 105106 - 108
843ASNASNILEILE2DD103 - 105106 - 108
114PROPROGLYGLY5AA111 - 116114 - 119
214PROPROGLYGLY5CC111 - 116114 - 119
314PROPROGLYGLY5DD111 - 116114 - 119
115ASPASPPHEPHE4AA20 - 2223 - 25
215ASPASPPHEPHE4BB20 - 2223 - 25
325ASNASNTHRTHR1AA23 - 2726 - 30
425ASNASNTHRTHR1BB23 - 2726 - 30
116ASPASPPHEPHE4CC20 - 2223 - 25
216ASPASPPHEPHE4DD20 - 2223 - 25
326ASNASNTHRTHR1CC23 - 2726 - 30
426ASNASNTHRTHR1DD23 - 2726 - 30

NCS ensembles :
ID
1
2
3
4
5
6
Detailsmonomer is biological unit

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Components

#1: Protein
FLOWERING LOCUS T protein


Mass: 19376.809 Da / Num. of mol.: 4 / Mutation: d42n, c107s, c164s
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: FT / Plasmid: pet-28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): bl21 (de3) / References: UniProt: Q9SXZ2
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.1
Details: 0.14M Ammonium Sulfate, 38% w/v PEG 5000 MME, 0.1M MES, pH 7.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 1.488 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 7, 2003
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. obs: 21870 / % possible obs: 93.2 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 12.05
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.17 / Mean I/σ(I) obs: 3.8 / % possible all: 66.2

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: arabidopsis thaliana terminal flower 1 (tfl1)

Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.908 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22611 1104 5 %RANDOM
Rwork0.18129 ---
obs0.18358 20788 93.74 %-
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: 22.073 Å2
Baniso -1Baniso -2Baniso -3
1--0.72 Å2-1.01 Å2-0.87 Å2
2--0.3 Å24.13 Å2
3----0.49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5202 0 15 195 5412
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215350
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.41.9447318
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9015645
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0950.2813
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024208
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1980.22074
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2279
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2280.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3050.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.4381.53249
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.8425328
X-RAY DIFFRACTIONr_scbond_it1.26532101
X-RAY DIFFRACTIONr_scangle_it2.1154.51990
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A920tight positional0.080.05
12B920tight positional0.090.05
13C920tight positional0.090.05
14D920tight positional0.090.05
21A137tight positional0.030.05
31C148tight positional0.190.05
51A40tight positional0.020.05
61C40tight positional0.020.05
21A4medium positional0.090.5
31C13medium positional0.10.5
41A24medium positional0.160.5
42C24medium positional0.180.5
43D24medium positional0.060.5
51A26medium positional0.10.5
61C26medium positional0.040.5
11A69loose positional0.75
12B69loose positional0.955
13C69loose positional0.725
14D69loose positional0.85
21A7loose positional0.65
41A12loose positional0.595
42C12loose positional0.555
43D12loose positional0.45
11A920tight thermal0.080.5
12B920tight thermal0.080.5
13C920tight thermal0.080.5
14D920tight thermal0.090.5
21A137tight thermal0.080.5
31C148tight thermal0.070.5
51A40tight thermal0.040.5
61C40tight thermal0.050.5
21A4medium thermal0.282
31C13medium thermal0.52
41A24medium thermal0.72
42C24medium thermal0.392
43D24medium thermal0.632
51A26medium thermal0.142
61C26medium thermal0.322
11A69loose thermal2.5810
12B69loose thermal2.6510
13C69loose thermal210
14D69loose thermal3.0410
21A7loose thermal3.1610
41A12loose thermal0.7410
42C12loose thermal0.3910
43D12loose thermal0.7310
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.291 55
Rwork0.224 1043
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
13.30310.2030.22614.5032-0.08313.01390.0288-0.05560.03740.1161-0.0989-0.16680.00930.06590.07010.0387-0.00820.00010.0752-0.00110.020674.497710.826862.5845
23.53040.26170.28372.85290.52413.8291-0.00770.07180.06020.0559-0.01450.03050.019-0.14870.02220.04370.0038-0.00050.02680.0130.054937.227838.437634.2762
34.89970.53840.09323.6784-0.51943.2149-0.0153-0.13250.10890.09870.00250.0018-0.2360.07830.01280.06440.00380.00630.0463-0.00730.00747.773856.216213.7807
44.49380.06430.64622.7746-0.43294.19340.08610.0712-0.1606-0.1675-0.07430.04310.20490.0878-0.01180.0480.01090.00440.02260.01050.051163.971825.54439.7898
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1679 - 170
2X-RAY DIFFRACTION2BB6 - 1679 - 170
3X-RAY DIFFRACTION3CC6 - 1679 - 170
4X-RAY DIFFRACTION4DD6 - 1679 - 170

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