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Yorodumi- PDB-8ejv: The crystal structure of Pseudomonas putida PcaR in complex with ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8ejv | ||||||
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Title | The crystal structure of Pseudomonas putida PcaR in complex with succinate | ||||||
Components | Transcription regulatory protein (Pca regulon) | ||||||
Keywords | TRANSCRIPTION / Complex / Transcription Factor / Succinate / Gene Regulation | ||||||
Function / homology | Function and homology information 3,4-dihydroxybenzoate metabolic process / DNA-binding transcription repressor activity / protein-DNA complex / sequence-specific DNA binding / transcription cis-regulatory region binding / negative regulation of DNA-templated transcription / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Pseudomonas putida KT2440 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å | ||||||
Authors | Pham, C. / Skarina, T. / Di Leo, R. / Stogios, P.J. / Mahadevan, R. / Savchenko, A. | ||||||
Funding support | Canada, 1items
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Citation | Journal: To Be Published Title: The crystal structure of Pseudomonas putida PcaR in complex with succinate Authors: Pham, C. / Stogios, P.J. / Mahadevan, R. / Savchenko, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8ejv.cif.gz | 239.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8ejv.ent.gz | 172.3 KB | Display | PDB format |
PDBx/mmJSON format | 8ejv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ej/8ejv ftp://data.pdbj.org/pub/pdb/validation_reports/ej/8ejv | HTTPS FTP |
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-Related structure data
Related structure data | 2ia2S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 31778.303 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida KT2440 (bacteria) Strain: ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440 Gene: pcaR, PP_1375 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): -Magic / References: UniProt: Q88N41 |
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-Non-polymers , 5 types, 137 molecules
#2: Chemical | #3: Chemical | ChemComp-EDO / | #4: Chemical | ChemComp-PO4 / | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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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: 2.85 Å3/Da / Density % sol: 56.83 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Reservoir: 1.8 M ammonium phosphate monophosphate, 0.1 M succinic acid, pH 7, 1.25% w/v Benzyltriethylammonium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.925 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 24, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.925 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→37.21 Å / Num. obs: 26706 / % possible obs: 100 % / Redundancy: 10.3 % / Biso Wilson estimate: 58.04 Å2 / CC1/2: 1 / Rpim(I) all: 0.022 / Rrim(I) all: 0.071 / Net I/σ(I): 56.16 |
Reflection shell | Resolution: 2.5→2.54 Å / Num. unique obs: 1243 / CC1/2: 0.906 / Rpim(I) all: 0.193 / Rrim(I) all: 0.628 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2IA2 Resolution: 2.43→37.21 Å / SU ML: 0.2918 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.7458 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 67.26 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→37.21 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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