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- PDB-8hew: Potato 14-3-3 St14f -

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Basic information

Entry
Database: PDB / ID: 8hew
TitlePotato 14-3-3 St14f
Components
  • 14-3-3 protein
  • StFDL1 peptide
KeywordsPROTEIN BINDING / 14-3-3
Function / homology14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / 14-3-3 protein
Function and homology information
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 Å
AuthorsTaoka, K. / Kawahara, I. / Shinya, S. / Harada, K. / Muranaka, T. / Furuita, K. / Nakagawa, A. / Fujiwara, T. / Tsuji, H. / Kojima, C.
Funding support Japan, 1items
OrganizationGrant numberCountry
Ministry of Education, Culture, Sports, Science and Technology (Japan)17K07609, 16H06464, 16H06466, 17H05836, 19H04856, 20H03191, 16H02532, 21H04728, and 22H04978 Japan
CitationJournal: Plant J. / Year: 2022
Title: Multifunctional chemical inhibitors of the florigen activation complex discovered by structure-based high-throughput screening.
Authors: Taoka, K.I. / Kawahara, I. / Shinya, S. / Harada, K.I. / Yamashita, E. / Shimatani, Z. / Furuita, K. / Muranaka, T. / Oyama, T. / Terada, R. / Nakagawa, A. / Fujiwara, T. / Tsuji, H. / Kojima, C.
History
DepositionNov 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein
B: StFDL1 peptide


Theoretical massNumber of molelcules
Total (without water)27,3782
Polymers27,3782
Non-polymers00
Water00
1
A: 14-3-3 protein
B: StFDL1 peptide

A: 14-3-3 protein
B: StFDL1 peptide


Theoretical massNumber of molelcules
Total (without water)54,7564
Polymers54,7564
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area4310 Å2
ΔGint-30 kcal/mol
Surface area23630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.628, 121.628, 69.648
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein 14-3-3 protein / 14f protein


Mass: 26517.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: 30G / Production host: Escherichia coli (E. coli) / References: UniProt: P93785
#2: Protein/peptide StFDL1 peptide


Mass: 859.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Solanum tuberosum (potato)
Has ligand of interestY
Has protein modificationY

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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: 5.43 Å3/Da / Density % sol: 77.36 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 12% (w/ v) polyethylene glycol (PEG) 8000, 0.2M ammonium tartrate, pH 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Feb 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.59→50 Å / Num. obs: 18669 / % possible obs: 99.5 % / Redundancy: 7 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.041 / Rrim(I) all: 0.111 / Χ2: 1.62 / Net I/σ(I): 9.6 / Num. measured all: 131010
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.59-2.635.90.5618870.8670.2450.6150.96996.4
2.63-2.686.60.4869180.8950.20.5280.9699.4
2.68-2.736.60.4458990.9140.1830.4830.929100
2.73-2.796.70.3749480.9290.1520.4050.967100
2.79-2.856.80.3319210.9410.1340.3580.941100
2.85-2.926.90.3069380.960.1240.3310.97999.8
2.92-2.997.10.2689060.960.1060.2890.979100
2.99-3.077.20.239360.9730.0910.2481.145100
3.07-3.167.20.2159390.9750.0850.2321.206100
3.16-3.267.30.1829230.980.0710.1961.217100
3.26-3.387.30.159270.9850.0590.1621.364100
3.38-3.517.30.1269450.9890.050.1361.718100
3.51-3.677.30.1119460.9920.0430.1191.88100
3.67-3.877.30.0999230.9930.0390.1072.24899.9
3.87-4.117.20.0829440.9950.0320.0892.548100
4.11-4.437.20.0769370.9960.0290.0812.893100
4.43-4.877.20.0729450.9970.0270.0772.919100
4.87-5.587.30.0699490.9970.0260.0742.47199.6
5.58-7.027.30.0569620.9980.0220.0611.79798.9
7.02-506.80.0369760.9990.0150.0391.70996.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1O9C

1o9c


Resolution: 2.59→50 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2653 --RANDOM
Rwork0.2432 ---
obs-18669 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.59→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1881 0 0 0 1881

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