+Open data
-Basic information
Entry | Database: PDB / ID: 2yny | ||||||
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Title | Salmonella enterica SadA 255-302 fused to GCN4 adaptors (SadAK1) | ||||||
Components | GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN | ||||||
Keywords | MEMBRANE PROTEIN / FGG DOMAIN / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / CHIMERA | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding ...protein localization to nuclear periphery / FCERI mediated MAPK activation / Activation of the AP-1 family of transcription factors / response to amino acid starvation / mediator complex binding / negative regulation of ribosomal protein gene transcription by RNA polymerase II / positive regulation of cellular response to amino acid starvation / nitrogen catabolite activation of transcription from RNA polymerase II promoter / Oxidative Stress Induced Senescence / TFIID-class transcription factor complex binding / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / amino acid biosynthetic process / cellular response to amino acid starvation / cell outer membrane / RNA polymerase II transcription regulator complex / : / protein transport / DNA-binding transcription activator activity, RNA polymerase II-specific / RNA polymerase II-specific DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / regulation of cell cycle / intracellular signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / negative regulation of transcription by RNA polymerase II / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | SACCHAROMYCES CEREVISIAE (brewer's yeast) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||
Authors | Hartmann, M.D. / Hernandez Alvarez, B. / Albrecht, R. / Lupas, A.N. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2012 Title: Complete Fiber Structures of Complex Trimeric Autotransporter Adhesins Conserved in Enterobacteria. Authors: Hartmann, M.D. / Grin, I. / Dunin-Horkawicz, S. / Deiss, S. / Linke, D. / Lupas, A.N. / Hernandez Alvarez, B. #1: Journal: Protein Eng.Des.Sel. / Year: 2008 Title: A New Expression System for Protein Crystallization Using Trimeric Coiled-Coil Adaptors. Authors: Hernandez Alvarez, B. / Hartmann, M.D. / Albrecht, R. / Lupas, A.N. / Zeth, K. / Linke, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yny.cif.gz | 146.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yny.ent.gz | 116.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yny.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yny_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 2yny_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 2yny_validation.xml.gz | 15.5 KB | Display | |
Data in CIF | 2yny_validation.cif.gz | 23.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yn/2yny ftp://data.pdbj.org/pub/pdb/validation_reports/yn/2yny | HTTPS FTP |
-Related structure data
Related structure data | 2ynzC 2yo0C 2yo1C 2yo2C 2yo3C 1gcmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11805.523 Da / Num. of mol.: 3 Fragment: GCN4 AT EITHER END, RESIDUES 250-278. ADHESIN, RESIDUES 255-302 Mutation: YES Source method: isolated from a genetically manipulated source Details: N- AND C-TERMINAL IN-REGISTER FUSION TO GCN4 ADAPTORS Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast), (gene. exp.) SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR TYPHIMURIUM (bacteria) Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03069, UniProt: Q8ZL64 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 36 % / Description: NONE |
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Crystal grow | Details: 16% (W/V) PEG 4000, 80 MM SODIUM ACETATE, 100 MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.8266 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 1, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8266 Å / Relative weight: 1 |
Reflection | Resolution: 1.35→38 Å / Num. obs: 57902 / % possible obs: 96 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 1.35→1.43 Å / Redundancy: 3.22 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 1.98 / % possible all: 89.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCM Resolution: 1.35→37.95 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.414 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.992 Å2
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Refinement step | Cycle: LAST / Resolution: 1.35→37.95 Å
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