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Yorodumi- PDB-3kto: Crystal structure of response regulator receiver protein from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kto | ||||||
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Title | Crystal structure of response regulator receiver protein from Pseudoalteromonas atlantica | ||||||
Components | Response regulator receiver protein | ||||||
Keywords | transcription regulator / Response regulator receiver protein / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudoalteromonas atlantica T6c (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.98 Å | ||||||
Authors | Damodharan, L. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of response regulator receiver protein from Pseudoalteromonas atlantica Authors: Damodharan, L. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kto.cif.gz | 84.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kto.ent.gz | 68.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kto.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/3kto ftp://data.pdbj.org/pub/pdb/validation_reports/kt/3kto | 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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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Details | authors state that the biological assembly is a trimer |
-Components
#1: Protein | Mass: 15440.897 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudoalteromonas atlantica T6c (bacteria) Strain: Strain T6c/BAA-1087 / Gene: Patl_2095 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q15U25 #2: Water | ChemComp-HOH / | |
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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: 2.39 Å3/Da / Density % sol: 48.44 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.2M Sodium chloride, 0.1M HEPES pH 7.5, 25% w/v Polyethylene Glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2009 / Details: mirror |
Radiation | Monochromator: Si(111)channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.98→50 Å / Num. all: 30894 / Num. obs: 30894 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 24 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 1.98→2.1 Å / Redundancy: 24.8 % / Rmerge(I) obs: 0.369 / Mean I/σ(I) obs: 2 / Num. unique all: 4285 / % possible all: 88.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.98→40.55 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 102203.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 45.9926 Å2 / ksol: 0.342456 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.98→40.55 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.98→2.1 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
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Xplor file |
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