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Yorodumi- PDB-2yo1: Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yo1 | ||||||
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Title | Salmonella enterica SadA 1049-1304 fused to GCN4 adaptors (SadAK9- cfII) | ||||||
Components | GENERAL CONTROL PROTEIN GCN4, PUTATIVE INNER MEMBRANE PROTEIN | ||||||
Keywords | MEMBRANE PROTEIN / HANS MOTIF / YADA-LIKE HEAD / YLHEAD / HEAD INSERT MOTIF / HIM / TRIMERIC AUTOTRANSPORTER ADHESIN / TAA / CHIMERA | ||||||
Function / homology | Function and homology information protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II ...protein localization to nuclear periphery / 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 / TFIID-class transcription factor complex binding / amino acid biosynthetic process / positive regulation of transcription initiation by RNA polymerase II / positive regulation of RNA polymerase II transcription preinitiation complex assembly / 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 / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / 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: 3.1 Å | ||||||
Authors | Hartmann, M.D. / Hernandez Alvarez, B. / 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. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yo1.cif.gz | 304.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yo1.ent.gz | 248.6 KB | Display | PDB format |
PDBx/mmJSON format | 2yo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yo/2yo1 ftp://data.pdbj.org/pub/pdb/validation_reports/yo/2yo1 | HTTPS FTP |
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-Related structure data
Related structure data | 2ynyC 2ynzC 2yo0C 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 34005.398 Da / Num. of mol.: 3 Fragment: RESIDUES 1049-1304 FUSED TO GCN4 ADAPTORS, RESIDUES 250-278 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: Chemical | ChemComp-CL / | Sequence details | C-TERMINAL HIS-TAG | |
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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: 2.4 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 15 % (V/V) BUTANEDIOL, 100 MM SODIUM ACETATE PH 4.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 19, 2009 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→39.1 Å / Num. obs: 18792 / % possible obs: 96.9 % / Redundancy: 2.31 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.93 |
Reflection shell | Resolution: 3.1→3.28 Å / Redundancy: 2.35 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.35 / % possible all: 94.6 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GCM Resolution: 3.1→38.64 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.851 / SU B: 55.961 / SU ML: 0.455 / Cross valid method: THROUGHOUT / ESU R Free: 0.58 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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: 55.628 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→38.64 Å
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Refine LS restraints |
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