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- PDB-7xbq: Crystal structure of potato 14-3-3 protein St14f -

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Basic information

Entry
Database: PDB / ID: 7xbq
TitleCrystal structure of potato 14-3-3 protein St14f
ComponentsPutative 14-3-3 protein
KeywordsPLANT PROTEIN
Function / homology
Function and homology information


14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 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 domain / Delta-Endotoxin; domain 1 / 14-3-3 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 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSolanum tuberosum (potato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsHarada, K. / Kojima, C. / Yamashita, E. / Nakagawa, A.
Funding support Japan, 4items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05836 Japan
Japan Society for the Promotion of Science (JSPS)19H04856 Japan
Japan Society for the Promotion of Science (JSPS)20H03191 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101072 Japan
CitationJournal: Sci Rep / Year: 2022
Title: Crystal structure of potato 14-3-3 protein St14f revealed the importance of helix I in StFDL1 recognition.
Authors: Harada, K.I. / Furuita, K. / Yamashita, E. / Taoka, K.I. / Tsuji, H. / Fujiwara, T. / Nakagawa, A. / Kojima, C.
History
DepositionMar 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative 14-3-3 protein
B: Putative 14-3-3 protein
C: Putative 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)87,7343
Polymers87,7343
Non-polymers00
Water00
1
A: Putative 14-3-3 protein

A: Putative 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)58,4892
Polymers58,4892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area2140 Å2
ΔGint-12 kcal/mol
Surface area23350 Å2
MethodPISA
2
B: Putative 14-3-3 protein

C: Putative 14-3-3 protein


Theoretical massNumber of molelcules
Total (without water)58,4892
Polymers58,4892
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1/2,y-1/2,-z1
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area23770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)230.198, 105.281, 60.987
Angle α, β, γ (deg.)90.000, 104.840, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Putative 14-3-3 protein


Mass: 29244.703 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Solanum tuberosum (potato) / Gene: 30G, 14-3-3, St14f / Production host: Escherichia coli (E. coli) / References: UniProt: P93785

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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: 4.07 Å3/Da / Density % sol: 69.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 8000, Ammonium tartrate, HEPES

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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 MX225HE / Detector: CCD / Date: Oct 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.45→47.6 Å / Num. obs: 51160 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.981 / Rmerge(I) obs: 0.063 / Net I/σ(I): 28.8
Reflection shellResolution: 2.45→2.49 Å / Rmerge(I) obs: 0.442 / Num. unique obs: 2531

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Processing

Software
NameVersionClassification
SCALAdata scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3axy

3axy


Resolution: 2.45→47.58 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.896 / SU B: 20.497 / SU ML: 0.203 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.777 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2768 2573 5 %RANDOM
Rwork0.209 ---
obs0.2123 48586 99.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 255.36 Å2 / Biso mean: 73.712 Å2 / Biso min: 32.79 Å2
Baniso -1Baniso -2Baniso -3
1-7.05 Å20 Å2-1.02 Å2
2---7.15 Å2-0 Å2
3---0.57 Å2
Refinement stepCycle: final / Resolution: 2.45→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5347 0 0 0 5347
Num. residues----701
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0135422
X-RAY DIFFRACTIONr_bond_other_d0.0030.0155002
X-RAY DIFFRACTIONr_angle_refined_deg1.8441.647322
X-RAY DIFFRACTIONr_angle_other_deg1.4091.57911494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8465698
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.11722.705281
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.12315944
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0921536
X-RAY DIFFRACTIONr_chiral_restr0.0830.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026221
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021207
X-RAY DIFFRACTIONr_rigid_bond_restr6.164310424
LS refinement shellResolution: 2.454→2.518 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 168 -
Rwork0.319 3437 -
all-3605 -
obs--95.65 %
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)
12.0151-0.1451-0.23550.8303-0.19082.2552-0.1564-0.06790.22060.1023-0.03560.0907-0.4468-0.3910.1920.11690.0564-0.03410.3614-0.06580.2507-18.976-0.42541.4767
22.38570.89390.00671.57990.29821.6943-0.13-0.1315-0.0142-0.1064-0.0086-0.12780.24220.05580.13860.0733-0.03130.04280.3318-0.02290.2196-38.5784-25.864625.5933
32.4119-1.20350.98341.5177-0.81873.28750.23150.1188-0.6525-0.173-0.13160.2110.7675-0.0301-0.09980.25840.16750.00170.41790.01460.2497-50.7563-0.1452-21.9204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 233
2X-RAY DIFFRACTION2B1 - 235
3X-RAY DIFFRACTION3C1 - 233

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