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Yorodumi- PDB-3hdg: Crystal structure of the N-terminal domain of an uncharacterized ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3hdg | ||||||
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Title | Crystal structure of the N-terminal domain of an uncharacterized protein (WS1339) from Wolinella succinogenes | ||||||
Components | uncharacterized protein | ||||||
Keywords | structural genomics / unknown function / two-component sensor activity / response regulator / PSI-II / 11227f / NYSGXRC / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Wolinella succinogenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.27 Å | ||||||
Authors | Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: To be Published Title: Crystal structure of the N-terminal domain of an uncharacterized protein (WS1339) from Wolinella succinogenes Authors: Eswaramoorthy, S. / 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 | 3hdg.cif.gz | 107.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hdg.ent.gz | 87.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hdg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hdg_validation.pdf.gz | 455.5 KB | Display | wwPDB validaton report |
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Full document | 3hdg_full_validation.pdf.gz | 467 KB | Display | |
Data in XML | 3hdg_validation.xml.gz | 21.5 KB | Display | |
Data in CIF | 3hdg_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hd/3hdg ftp://data.pdbj.org/pub/pdb/validation_reports/hd/3hdg | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 15826.573 Da / Num. of mol.: 4 / Fragment: N-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Wolinella succinogenes (bacteria) / Gene: WS1339 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MRH8 #2: Chemical | ChemComp-MG / #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: 2.15 Å3/Da / Density % sol: 42.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 30% PEG MME 550, 50mM Magnesium Chloride, 100mM HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2009 |
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: 2.27→40.22 Å / Num. all: 24794 / Num. obs: 24794 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 2.27→2.35 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.56 / Num. unique all: 2370 / % possible all: 95.6 |
-Processing
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Refinement | Method to determine structure: SAD / Resolution: 2.27→38.53 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.27→38.53 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.27→2.41 Å / Rfactor Rfree error: 9.028
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