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Yorodumi- PDB-4gw9: Structure of a bacteriophytochrome and light-stimulated protomer ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gw9 | |||||||||
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Title | Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor | |||||||||
Components | bacteriophytochrome | |||||||||
Keywords | SIGNALING PROTEIN / PHOTORECEPTOR / PAS/PAC SENSOR / BACTERIOPBHYTOCHROME / BACTERIOPHYTOCHROME PHOTOSENSORY AND C-TERMINAL OUTPUT TRANSDUCING DOMAINS / GENE REPRESSOR RPPPSR2 / photosensory core domain and PAS/PAC domain / Light signaling / PpsR2 | |||||||||
Function / homology | Function and homology information detection of visible light / photoreceptor activity / regulation of DNA-templated transcription / ATP binding Similarity search - Function | |||||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å | |||||||||
Authors | Bellini, D. / Papiz, M.Z. | |||||||||
Citation | Journal: Structure / Year: 2012 Title: Structure of a bacteriophytochrome and light-stimulated protomer swapping with a gene repressor. Authors: Bellini, D. / Papiz, M.Z. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gw9.cif.gz | 981 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gw9.ent.gz | 847.2 KB | Display | PDB format |
PDBx/mmJSON format | 4gw9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gw/4gw9 ftp://data.pdbj.org/pub/pdb/validation_reports/gw/4gw9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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 oper:
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-Components
#1: Protein | Mass: 72958.180 Da / Num. of mol.: 4 / Fragment: N-terminal 70 kDa fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: RPA1537 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: B3Q7C0, histidine kinase #2: Chemical | ChemComp-BLA / #3: Water | ChemComp-HOH / | Sequence details | THE FULL LENGTH PROTEIN WITH N-HIS6TAG-(1-730) WAS EXPRESSED. HOWEVER, RESIDUES 636-730 WERE LOST ...THE FULL LENGTH PROTEIN WITH N-HIS6TAG-(1-730) WAS EXPRESSED. HOWEVER, RESIDUES 636-730 WERE LOST DURING PURIFICATI | Source details | THE PROTEIN SOURCE IS RHODOPSEUDOMONAS PALUSTRIS, STRAIN CGA009 AND THE GENE IS RPA1537. THIS GENE ...THE PROTEIN SOURCE IS RHODOPSEUD | |
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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: 3.69 Å3/Da / Density % sol: 66.7 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8 Details: PROTEIN CONCENTRATION 20 MG/ML, 4% POLY-GAMMA-GLUTAMIC ACID POLYMER, 100 MM TRISHCL PH 8, 0.4 M NIACINAMIDE, 200 MM KBR, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-Data collection
Diffraction |
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Diffraction source |
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Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Feb 24, 2011 | ||||||||||||||||||
Radiation |
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Radiation wavelength |
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Reflection | Resolution: 2.8→74 Å / Num. obs: 97789 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Rsym value: 0.066 / Net I/σ(I): 9.6 | ||||||||||||||||||
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.63 / % possible all: 96.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 2.9→15 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 29.769 / SU ML: 0.269 / Cross valid method: THROUGHOUT / ESU R: 1.253 / ESU R Free: 0.352 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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 mean: 30.01 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→2.972 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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