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- PDB-1o9d: Structural view of a fungal toxin acting on a 14-3-3 regulatory c... -

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Basic information

Entry
Database: PDB / ID: 1o9d
TitleStructural view of a fungal toxin acting on a 14-3-3 regulatory complex
Components
  • 14-3-3-LIKE PROTEIN C
  • PLASMA MEMBRANE H+ ATPASE
KeywordsPROTEIN BINDING / PROTEIN-BINDING / FUSICOCCIN / 14-3-3 FAMILY / ACTIVATING DRUG / PLANT PLASMA MEMBRANE (H+)ATPASE
Function / homology
Function and homology information


P-type proton-exporting transporter activity / regulation of intracellular pH / protein localization / signal transduction / ATP hydrolysis activity / ATP binding / plasma membrane / 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 / P-type ATPase / P-type ATPase, transmembrane domain superfamily / haloacid dehalogenase-like hydrolase / HAD superfamily / HAD-like superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3-like protein C / Plasma membrane H+ ATPase
Similarity search - Component
Biological speciesNICOTIANA TABACUM (common tobacco)
NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 / Derived calculations / 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE


Theoretical massNumber of molelcules
Total (without water)30,0772
Polymers30,0772
Non-polymers00
Water3,153175
1
A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE

A: 14-3-3-LIKE PROTEIN C
P: PLASMA MEMBRANE H+ ATPASE


Theoretical massNumber of molelcules
Total (without water)60,1534
Polymers60,1534
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_655-x+y+1,y,-z+1/21
Buried area4250 Å2
ΔGint-24.83 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.126, 110.126, 136.464
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsTHE ENTRY IS A DIMER OF CHAIN A, WHICH IN COMPLEX WITH PEPTIDE CHAIN P MAKES IT APPEAR AS A TETRAMERIC COMPLEX OF CHAINS A AND P.

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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: Protein/peptide PLASMA MEMBRANE H+ ATPASE


Mass: 676.610 Da / Num. of mol.: 1 / Fragment: RESIDUES 436-440 / Source method: obtained synthetically
Source: (synth.) NICOTIANA PLUMBAGINIFOLIA (curled-leaved tobacco)
References: UniProt: Q40409
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
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: 3.97 Å3/Da / Density % sol: 69.03 %
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: 0.979
DetectorDate: Dec 15, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→10 Å / Num. obs: 21328 / % possible obs: 95.5 % / Observed criterion σ(I): 2 / Redundancy: 6.2 % / Biso Wilson estimate: 59 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 18.1
Reflection shellResolution: 2.3→2.4 Å / Rmerge(I) obs: 0.351 / Mean I/σ(I) obs: 4 / % possible all: 98.1
Reflection
*PLUS
Lowest resolution: 10 Å / Num. measured all: 131256
Reflection shell
*PLUS
% possible obs: 98.1 %

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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: 2.3→19.38 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3077461.25 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.244 1041 5 %RANDOM
Rwork0.21 ---
obs0.21 21283 95.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 57.9462 Å2 / ksol: 0.340913 e/Å3
Displacement parametersBiso mean: 60.7 Å2
Baniso -1Baniso -2Baniso -3
1-8.16 Å25.52 Å20 Å2
2--8.16 Å20 Å2
3----16.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.3 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 0 175 2050
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.023
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_deg2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.28
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: 2.3→2.44 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.309 153 4.3 %
Rwork0.284 3396 -
obs--97.8 %
Refinement
*PLUS
Lowest resolution: 10 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.28

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