+Open data
-Basic information
Entry | Database: PDB / ID: 3kht | ||||||
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Title | Crystal structure of response regulator from Hahella chejuensis | ||||||
Components | Response regulator | ||||||
Keywords | SIGNALING PROTEIN / Response regulator / PSI-II / 11023k / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC / DNA-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Hahella chejuensis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å | ||||||
Authors | Bagaria, A. / 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 from Hahella chejuensis Authors: Bagaria, A. / 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 | 3kht.cif.gz | 36.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kht.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3kht.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kh/3kht ftp://data.pdbj.org/pub/pdb/validation_reports/kh/3kht | 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 16386.117 Da / Num. of mol.: 1 / Fragment: sequence database residues 13-145 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hahella chejuensis (bacteria) / Strain: KCTC 2396 / Gene: HCH_02875 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q2SI73 |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.88 Å3/Da / Density % sol: 57.25 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 0.1M NaCl, 0.1M HEPES pH 7.5, 1.6M Ammonium Sulphate, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.979 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2009 / Details: MIRRORS |
Radiation | Monochromator: SI(111)CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→39.75 Å / Num. obs: 11490 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 40 % / Biso Wilson estimate: 41.9 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 41.3 % / Rmerge(I) obs: 0.403 / Mean I/σ(I) obs: 11.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.1→39.75 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.387 / SU ML: 0.143 / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.192 / 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: 37.22 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→39.75 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.15 Å / Total num. of bins used: 20
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