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Yorodumi- PDB-2c9c: Structural basis of the nucleotide driven conformational changes ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c9c | ||||||
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Title | Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF | ||||||
Components | PSP OPERON TRANSCRIPTIONAL ACTIVATOR | ||||||
Keywords | TRANSCRIPTION REGULATION / BACTERIAL SIGMA54 ACTIVATOR / ATPASE / ATP-BINDING / DNA-BINDING / SENSORY TRANSDUCTION / TWO-COMPONENT REGULATORY SYSTEM | ||||||
Function / homology | Function and homology information regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding ...regulation of cellular response to stress / phosphorelay signal transduction system / transcription regulator complex / sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / ATP hydrolysis activity / DNA binding / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ESCHERICHIA COLI (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Rappas, M. / Schumacher, J. / Niwa, H. / Buck, M. / Zhang, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2006 Title: Structural Basis of the Nucleotide Driven Conformational Changes in the Aaa(+) Domain of Transcription Activator Pspf. Authors: Rappas, M. / Schumacher, J. / Niwa, H. / Buck, M. / Zhang, X. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c9c.cif.gz | 68.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c9c.ent.gz | 49 KB | Display | PDB format |
PDBx/mmJSON format | 2c9c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c9c_validation.pdf.gz | 788.1 KB | Display | wwPDB validaton report |
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Full document | 2c9c_full_validation.pdf.gz | 790.1 KB | Display | |
Data in XML | 2c9c_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | 2c9c_validation.cif.gz | 18.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/2c9c ftp://data.pdbj.org/pub/pdb/validation_reports/c9/2c9c | HTTPS FTP |
-Related structure data
Related structure data | 2c96C 2c98C 2c99C 2bjwS 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: 29901.178 Da / Num. of mol.: 1 / Fragment: AAA DOMAIN, RESIDUES 1-265 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: K12 / Plasmid: PET28B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): B834 / References: UniProt: P37344 |
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#2: Chemical | ChemComp-MG / |
#3: Chemical | ChemComp-ATP / |
#4: Water | ChemComp-HOH / |
Compound details | TRANSCRIPTIONAL ACTIVATOR FOR THE PHAGE SHOCK PROTEIN (PSP) OPERON (PSPABCE) ENGINEERED RESIDUE IN ...TRANSCRIPT |
Sequence details | MUTATION OF RESIDUE R227 INTO AN ALANINE AND DISORDERED |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47 % |
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Crystal grow | pH: 8 / Details: 2M AMMONIUM FORMATE, 0.1 M HEPES PH 8.0, 5% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.933 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 4, 2005 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→100 Å / Num. obs: 16682 / % possible obs: 98.8 % / Observed criterion σ(I): 3 / Redundancy: 7.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 26.7 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.25 / Mean I/σ(I) obs: 4.7 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BJW Resolution: 2.1→95.35 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.832 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGION HAVE NOT BEEN MODELLED AND DISORDERED RESIDUES HAVE BEEN MODELLED AS ALANINES
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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: 24.42 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→95.35 Å
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Refine LS restraints |
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