+Open data
-Basic information
Entry | Database: PDB / ID: 4whe | ||||||
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Title | Crystal structure of E. coli phage shock protein A (PspA 1-144) | ||||||
Components | Phage shock protein A | ||||||
Keywords | SIGNALING PROTEIN / PspA/IM30 family / AAA+ protein regulation / transcriptional regulation / stress inducible Psp system / phage shock response / coiled-coil / sigma 54 promoter / transcription initiation | ||||||
Function / homology | Function and homology information phage shock / cell pole / extrinsic component of cytoplasmic side of plasma membrane / phospholipid binding / negative regulation of DNA-binding transcription factor activity / response to heat / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Parthier, C. / Schoepfel, M. / Stubbs, M.T. / Osadnik, H. / Brueser, T. | ||||||
Citation | Journal: Mol.Microbiol. / Year: 2015 Title: PspF-binding domain PspA1-144 and the PspAF complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins. Authors: Osadnik, H. / Schopfel, M. / Heidrich, E. / Mehner, D. / Lilie, H. / Parthier, C. / Risselada, H.J. / Grubmuller, H. / Stubbs, M.T. / Bruser, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4whe.cif.gz | 73.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4whe.ent.gz | 54.3 KB | Display | PDB format |
PDBx/mmJSON format | 4whe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whe ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 17476.092 Da / Num. of mol.: 1 / Fragment: UNP residues 1-144 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: pspA, Z2482, ECs1881 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BW25113 / References: UniProt: P0AFM7, UniProt: P0AFM6*PLUS |
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#2: Chemical | ChemComp-TRS / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.36 % |
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Crystal grow | Temperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 0.1 M HEPES/NaOH, 10% (w/v) PEG 6000, 5% (v/v) MPD l |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841, 0.97981, 0.979927,0.975915 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2013 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Number: 48941 / Rmerge(I) obs: 0.047 / Χ2: 1.47 / D res high: 2.01 Å / D res low: 39.73 Å / Num. obs: 22364 / % possible obs: 96.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.8→39.73 Å / Num. obs: 15969 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 37.195 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.037 / Χ2: 0.967 / Net I/σ(I): 20.46 / Num. measured all: 54081 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: 0
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→39.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2745 / WRfactor Rwork: 0.2186 / FOM work R set: 0.6813 / SU B: 9.683 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1351 / SU Rfree: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.138 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.08 Å2 / Biso mean: 54.663 Å2 / Biso min: 22.09 Å2
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Refinement step | Cycle: final / Resolution: 1.8→39.73 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Details: coil 2 / Origin x: 5.048 Å / Origin y: -1.66 Å / Origin z: 57.218 Å
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