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Yorodumi- PDB-3hv2: Crystal structure of signal receiver domain OF HD domain-containi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hv2 | ||||||
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Title | Crystal structure of signal receiver domain OF HD domain-containing protein FROM Pseudomonas fluorescens Pf-5 | ||||||
Components | Response regulator/HD domain protein | ||||||
Keywords | SIGNALING PROTEIN / RESPONSE REGULATOR/HD DOMAIN PROTEIN / PSI-2 / NYSGXRC / STRUCTURAL GENOMICS / PROTEIN STRUCTURE INITIATIVE / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS / SIGNAL RECOGNITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas fluorescens Pf-5 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å | ||||||
Authors | Patskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Miller, S. / 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 HD domain-containing protein 3 FROM Pseudomonas fluorescens Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Miller, S. / 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 | 3hv2.cif.gz | 77.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hv2.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hv2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hv/3hv2 ftp://data.pdbj.org/pub/pdb/validation_reports/hv/3hv2 | 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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Unit cell |
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-Components
#1: Protein | Mass: 17612.074 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-143 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas fluorescens Pf-5 (bacteria) Strain: PF-5 / Gene: PFL_4895 / Plasmid: BC-PSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-CODON+RIL(STRATAGENE) / References: UniProt: Q4K707 #2: Chemical | #3: 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 Å3/Da / Density % sol: 38.59 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: 100MM BIS-TRIS-HCL, PH 5.5, 25% PEG3350, 200MM LITHIUM SULFATE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9789 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 12, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9789 Å / Relative weight: 1 |
Reflection | Resolution: 1.491→50 Å / Num. obs: 46427 / % possible obs: 98.5 % / Observed criterion σ(I): -5 / Redundancy: 2.9 % / Biso Wilson estimate: 14.292 Å2 / Rsym value: 0.059 / Net I/σ(I): 8.5 |
Reflection shell | Resolution: 1.49→1.54 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.154 / Mean I/σ(I) obs: 2.1 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.5→40 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.077 / SU ML: 0.042 / Cross valid method: THROUGHOUT / ESU R: 0.07 / ESU R Free: 0.072 / 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: 18.349 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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