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- PDB-1o9c: Structural view of a fungal toxin acting on a 14-3-3 regulatory c... -

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Basic information

Entry
Database: PDB / ID: 1o9c
TitleStructural view of a fungal toxin acting on a 14-3-3 regulatory complex
Components14-3-3-LIKE PROTEIN C
KeywordsPROTEIN BINDING / FUSICOCCIN / 14-3-3 FAMILY / ACTIVATING DRUG / PLANT PLASMA MEMBRANE (H+)ATPASE
Function / homology
Function and homology information


signal transduction / cytoplasm
Similarity search - Function
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
CITRATE ANION / 14-3-3-like protein C
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C.
CitationJournal: Embo J. / Year: 2003
Title: Structural View of a Fungal Toxin Acting on a 14-3-3 Regulatory Complex
Authors: Wurtele, M. / Jelich-Ottmann, C. / Wittinghofer, A. / Oecking, C.
History
DepositionDec 12, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 6, 2003Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3-LIKE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6253
Polymers29,4001
Non-polymers2252
Water1,18966
1
A: 14-3-3-LIKE PROTEIN C
hetero molecules

A: 14-3-3-LIKE PROTEIN C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2496
Polymers58,8002
Non-polymers4494
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
MethodPQS
Unit cell
Length a, b, c (Å)109.231, 109.231, 135.865
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein 14-3-3-LIKE PROTEIN C


Mass: 29399.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GENE BANK AAC49892 / Source: (gene. exp.) NICOTIANA TABACUM (common tobacco) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P93343
#2: Chemical ChemComp-FLC / CITRATE ANION / Citric acid


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 3.98 Å3/Da / Density % sol: 69.09 %
Crystal growpH: 6.4 / Details: PEG400, CITRATE PH 4.7, 0.2 MM AMMONIUM ACETATE
Crystal grow
*PLUS
pH: 4.7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
121 %PEG4001reservoir
20.1 mMcitrate1reservoirpH4.7
30.2 mMammonium acetate1reservoirpH7.0
410 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8459
DetectorDate: Nov 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8459 Å / Relative weight: 1
ReflectionResolution: 2.6→10 Å / Num. obs: 15163 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 13.6 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 33.1
Reflection shellResolution: 2.6→2.7 Å / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 8.2 / % possible all: 99.4
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 205883
Reflection shell
*PLUS
% possible obs: 99.4 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
XDSdata reduction
XDSdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A4O

1a4o


Resolution: 2.6→19.75 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3345536.73 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 758 5 %RANDOM
Rwork0.222 ---
obs0.222 15155 99.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.8863 Å2 / ksol: 0.340786 e/Å3
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-11.48 Å28.64 Å20 Å2
2--11.48 Å20 Å2
3----22.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1838 0 14 66 1918
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.351 120 5 %
Rwork0.282 2282 -
obs--99.1 %
Refinement
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 10 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg17
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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