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- PDB-2o02: Phosphorylation independent interactions between 14-3-3 and Exoen... -

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Basic information

Entry
Database: PDB / ID: 2o02
TitlePhosphorylation independent interactions between 14-3-3 and Exoenzyme S: from structure to pathogenesis
Components
  • 14-3-3 protein zeta/delta
  • ExoS (416-430) peptide
KeywordsPROTEIN BINDING/TOXIN / 14-3-3 / adapter protein / ExoS / pathogen / PROTEIN BINDING-TOXIN COMPLEX
Function / homology
Function and homology information


Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling ...Golgi reassembly / regulation of synapse maturation / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / negative regulation of innate immune response / regulation of ERK1 and ERK2 cascade / protein sequestering activity / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / cadherin binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / 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
BENZOIC ACID / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsOttmann, C. / Yasmin, L. / Weyand, M. / Hauser, A.R. / Wittinghofer, A. / Hallberg, B.
CitationJournal: Embo J. / Year: 2007
Title: Phosphorylation-independent interaction between 14-3-3 and exoenzyme S: from structure to pathogenesis
Authors: Ottmann, C. / Yasmin, L. / Weyand, M. / Veesenmeyer, J.L. / Diaz, M.H. / Palmer, R.H. / Francis, M.S. / Hauser, A.R. / Wittinghofer, A. / Hallberg, B.
History
DepositionNov 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 14-3-3 protein zeta/delta
B: 14-3-3 protein zeta/delta
P: ExoS (416-430) peptide
Q: ExoS (416-430) peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,6136
Polymers55,3694
Non-polymers2442
Water12,989721
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.330, 72.238, 125.664
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 14-3-3 protein zeta/delta / Protein kinase C inhibitor protein 1 / KCIP-1


Mass: 26316.764 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: YWHAZ / Plasmid: pGEX 2TK / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P63104
#2: Protein/peptide ExoS (416-430) peptide


Mass: 1367.486 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: Chemically synthesized.
#3: Chemical ChemComp-BEZ / BENZOIC ACID / Benzoic acid


Mass: 122.121 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 721 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 285 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97883 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 3, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 1.5→25 Å / Num. all: 103943 / Num. obs: 103943 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 26.659 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 16.21
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obs% possible allNum. measured obsNum. unique all
1.5-1.60.3143.6298.6
2.3-2.40.12913.599.3206003436
2.4-2.50.11215.199.4174812922
2.5-30.0819.699.6571949527
3-40.03836.899.8458697667
4-50.02751100165172777
5-60.02849.599.874181258
6-100.02259.198.977661358
100.01966.992.51234234

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Phasing

Phasing MR
Highest resolutionLowest resolution
Rotation4 Å19.94 Å
Translation4 Å19.94 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
MAR345data collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→19.74 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.121 / SU ML: 0.052 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.212 5198 5 %RANDOM
Rwork0.147 ---
obs0.151 103941 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.548 Å2
Baniso -1Baniso -2Baniso -3
1--0.35 Å20 Å20 Å2
2---0.45 Å20 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.5→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4143 0 18 721 4882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.0224273
X-RAY DIFFRACTIONr_angle_refined_deg2.5581.9865827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3225592
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80425.596218
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.76915886
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7881527
X-RAY DIFFRACTIONr_chiral_restr0.1760.2646
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.023257
X-RAY DIFFRACTIONr_nbd_refined0.2420.22224
X-RAY DIFFRACTIONr_nbtor_refined0.3180.22920
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2470.2559
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3170.245
X-RAY DIFFRACTIONr_mcbond_it3.3811.52690
X-RAY DIFFRACTIONr_mcangle_it4.44924177
X-RAY DIFFRACTIONr_scbond_it6.41631847
X-RAY DIFFRACTIONr_scangle_it8.5934.51587
X-RAY DIFFRACTIONr_rigid_bond_restr3.8534537
X-RAY DIFFRACTIONr_sphericity_free14.2563721
X-RAY DIFFRACTIONr_sphericity_bonded9.91634161
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.292 377 -
Rwork0.175 7145 -
obs-7522 100 %

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