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Yorodumi- PDB-3cnb: Crystal structure of signal receiver domain of DNA binding respon... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cnb | ||||||
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Title | Crystal structure of signal receiver domain of DNA binding response regulator protein (merR) from Colwellia psychrerythraea 34H | ||||||
Components | DNA-binding response regulator, merR family | ||||||
Keywords | DNA BINDING PROTEIN / SIGNAL RECEIVER DOMAIN / PROTEIN STRUCTURE INITIATIVE / PSI-2 / New York SGX Research Center for Structural Genomics / NYSGXRC / STRUCTURAL GENOMICS / DNA-binding | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Colwellia psychrerythraea (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Patskovsky, Y. / Romero, R. / Freeman, J. / Hu, S. / Groshong, C. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of signal receiver domain of DNA binding response regulator (merR) from Colwellia psychrerythraea 34H. Authors: Patskovsky, Y. / Romero, R. / Freeman, J. / Hu, S. / Groshong, C. / Wasserman, S.R. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cnb.cif.gz | 86.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cnb.ent.gz | 66.8 KB | Display | PDB format |
PDBx/mmJSON format | 3cnb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/3cnb ftp://data.pdbj.org/pub/pdb/validation_reports/cn/3cnb | 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: PHE / Beg label comp-ID: PHE / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 4 / Auth seq-ID: 66 - 186 / Label seq-ID: 9 - 129
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Details | AUTHORS STATE THAT THE MONOMERIC ASSEMBLY OF THE BIOLOGICAL UNIT THAT IS SHOWN IN REMARK 350 IS PUTATIVE. |
-Components
#1: Protein | Mass: 15987.555 Da / Num. of mol.: 3 / Fragment: Signal receiver domain: Residues 61-192 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Colwellia psychrerythraea (bacteria) / Strain: 34H / Gene: CPS_4926 / Plasmid: BC-pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q47UF8 #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: 2.48 Å3/Da / Density % sol: 50.34 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 100mM HEPES pH 7.5, 25% PEG 6000, VAPOR DIFFUSION, SITTING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9793 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 7, 2008 |
Radiation | Monochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 32780 / % possible obs: 99.8 % / Observed criterion σ(I): -0.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 3.5 |
Reflection shell | Resolution: 2→2.07 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.91 / Mean I/σ(I) obs: 0.9 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.936 / SU B: 5.667 / SU ML: 0.151 / Cross valid method: THROUGHOUT / ESU R: 0.166 / ESU R Free: 0.161 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.122 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Ens-ID: 1 / Number: 923 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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