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Yorodumi- PDB-3t6k: Crystal structure of a putative response regulator (Caur_3799) fr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3t6k | ||||||
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Title | Crystal structure of a putative response regulator (Caur_3799) from Chloroflexus aurantiacus J-10-fl at 1.86 A resolution | ||||||
Components | Response regulator receiver | ||||||
Keywords | SIGNALING PROTEIN / Flavodoxin-like / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-BIOLOGY | ||||||
Function / homology | Function and homology information negative regulation of cell division / phosphorelay signal transduction system / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Chloroflexus aurantiacus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.86 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of a Hypothetical RESPONSE REGULATOR (Caur_3799) from Chloroflexus aurantiacus J-10-fl at 1.86 A resolution Authors: Joint Center for Structural Genomics (JCSG) / Shapiro, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3t6k.cif.gz | 117 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t6k.ent.gz | 95 KB | Display | PDB format |
PDBx/mmJSON format | 3t6k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t6/3t6k ftp://data.pdbj.org/pub/pdb/validation_reports/t6/3t6k | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 15161.036 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Chloroflexus aurantiacus (bacteria) / Strain: J-10-fl / Gene: Caur_3799 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A9WCL5 #2: Chemical | #3: Chemical | ChemComp-EDO / #4: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT (RESIDUES 1-135) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG ...THE CONSTRUCT (RESIDUES 1-135) WAS EXPRESSED WITH A PURIFICATI | |
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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: 3.73 Å3/Da / Density % sol: 66.98 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop Details: 20% polyethylene glycol 3350, 0.2M ammonium sulfate, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97916,0.91837,0.97876 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 20, 2011 Details: Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (ho rizontal focusing) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: single crystal Si(111) bent / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.86→46.117 Å / Num. obs: 39465 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.16 Å2 / Rmerge F obs: 0.145 / Rmerge(I) obs: 0.144 / Rrim(I) all: 0.15 / Net I/σ(I): 15.8 / Num. measured all: 472009 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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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: 1.86→46.117 Å / Cor.coef. Fo:Fc: 0.9613 / Cor.coef. Fo:Fc free: 0.955 / Occupancy max: 1 / Occupancy min: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED ...Details: 1. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 2. SULFATE AND ETHYLENE GLYCOL MODELED ARE PRESENT IN CRYSTALLIZATION/CRYO CONDITIONS. 3. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT.
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Displacement parameters | Biso max: 126.1 Å2 / Biso mean: 27.5286 Å2 / Biso min: 8.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.86→46.117 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.86→1.91 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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