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- PDB-2c96: Structural basis of the nucleotide driven conformational changes ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2c96 | ||||||
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Title | Structural basis of the nucleotide driven conformational changes in the AAA domain of transcription activator PspF | ||||||
![]() | PSP OPERON TRANSCRIPTIONAL ACTIVATOR | ||||||
![]() | TRANSCRIPTION REGULATION / BACTERIAL SIGMA54 ACTIVATOR / ATPASE / AAA DOMAIN / ACTIVATOR / ATP-BINDING / DNA-BINDING / NUCLEOTIDE-BINDING / SENSORY TRANSDUCTION / TWO-COMPONENT REGULATORY SYSTEM | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Rappas, M. / Schumacher, J. / Niwa, H. / Buck, M. / Zhang, X. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.6 KB | Display | ![]() |
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PDB format | ![]() | 47.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.9 KB | Display | ![]() |
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Full document | ![]() | 784.9 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 18.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2c98C ![]() 2c99C ![]() 2c9cC ![]() 2bjwS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 29987.295 Da / Num. of mol.: 1 / Fragment: AAA DOMAIN, RESIDUES 1-265 Source method: isolated from a genetically manipulated source Details: ATP / Source: (gene. exp.) ![]() ![]() ![]() ![]() | ||
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#2: Chemical | ChemComp-ATP / | ||
#3: Water | ChemComp-HOH / | ||
Compound details | TRANSCRIPTSequence details | DISORDERED | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 27, 2004 / 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: 1.8→100 Å / Num. obs: 26570 / % possible obs: 97.8 % / Observed criterion σ(I): 3 / Redundancy: 6 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 24 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 2.8 / % possible all: 93.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2BJW Resolution: 1.8→100 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.911 / SU B: 3.056 / SU ML: 0.095 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.128 / 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: 21.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→100 Å
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Refine LS restraints |
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