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Yorodumi- PDB-4e04: RpBphP2 chromophore-binding domain crystallized by homologue-dire... -
+Open data
-Basic information
Entry | Database: PDB / ID: 40000 | ||||||
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Title | RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis. | ||||||
Components | Bacteriophytochrome (Light-regulated signal transduction histidine kinase), PhyB1 | ||||||
Keywords | SIGNALING PROTEIN / Bacteriophytochrome chromophore binding domain / two component regulator / Response regulator RPA3017 / phosphorylation / phosphotransfer / TRANSFERASE | ||||||
Function / homology | Function and homology information detection of visible light / histidine kinase / photoreceptor activity / phosphorelay sensor kinase activity / regulation of DNA-templated transcription / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | Rhodopseudomonas palustris (phototrophic) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å | ||||||
Authors | Bellini, D. / Papiz, M.Z. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Dimerization properties of the RpBphP2 chromophore-binding domain crystallized by homologue-directed mutagenesis. 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 | 4e04.cif.gz | 275.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e04.ent.gz | 235.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e04.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e0/4e04 ftp://data.pdbj.org/pub/pdb/validation_reports/e0/4e04 | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 36187.113 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rhodopseudomonas palustris (phototrophic) Strain: CGA009 / Gene: phyB1, phyB2, RPA3015, RPA3016 / Plasmid: pET24a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q6N5G3 #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | MUTATIONS IN THE PDB FILE ARE AS DEFINED IN THE SEQADV RECORDS. NOTE THAT THERE IS AN INSERTED ...MUTATIONS IN THE PDB FILE ARE AS DEFINED IN THE SEQADV RECORDS. NOTE THAT THERE IS AN INSERTED RESIDUE ASN105 WHICH RESULTS IN THE SEQUENCE FOLLOWING THIS RESIDUE NUMBERED +1 MORE COMPARED TO THE NATIVE SEQUENCE (UNP Q6N5G3). IN THE MANUSCRIPT | |
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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: 2.16 Å3/Da / Density % sol: 43.17 % |
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Crystal grow | pH: 8.5 Details: 18% PEG3350, 0.2 mM MgCl2 or 0.2 mM CaCl2 and 0.1 Tris-HCl pH 8.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 1.79→74.8 Å / Num. obs: 59311 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rsym value: 0.023 / Net I/σ(I): 24.9 |
Reflection shell | Resolution: 1.79→1.84 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.537 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→15 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.95 / SU B: 7.672 / SU ML: 0.106 / Cross valid method: THROUGHOUT / ESU R: 0.13 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 50.84 Å2
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Refinement step | Cycle: LAST / Resolution: 1.79→15 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.79→1.84 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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