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Yorodumi- PDB-3hdv: Crystal structure of response regulator receiver protein from Pse... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdv | ||||||
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Title | Crystal structure of response regulator receiver protein from Pseudomonas putida | ||||||
Components | Response regulator | ||||||
Keywords | transcription regulator / Response regulator / PSI-II / 11224l / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas putida (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.09 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 receiver protein from Pseudomonas putida 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 | 3hdv.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdv.ent.gz | 86.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hdv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdv ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdv | 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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3 |
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Unit cell |
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Details | tetramer |
-Components
#1: Protein | Mass: 15240.009 Da / Num. of mol.: 4 / Fragment: Response Regulator Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas putida (bacteria) / Strain: KT2440 / Gene: PP_0355, PP0355 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q88QX9 #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: 3.1 Å3/Da / Density % sol: 60.3 % |
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Crystal grow | Temperature: 298 K / pH: 7.5 Details: 0.1M HEPES pH7.5, 0.8M Potassium Sodium Tartarate tetrahydrate, 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: 0.979 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 15, 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: 2.09→44.5 Å / Num. obs: 45411 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 39.7 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.1→2.18 Å / Redundancy: 13.1 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 5 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.09→44.5 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.931 / SU B: 4.178 / SU ML: 0.113 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.168 / ESU R Free: 0.159 / 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: 39.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.09→44.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.09→2.14 Å / Total num. of bins used: 20
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