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Yorodumi- PDB-3a39: Crystal Structure of High-Potential Iron-Sulfur Protein from Ther... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3a39 | ||||||
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Title | Crystal Structure of High-Potential Iron-Sulfur Protein from Thermochromatium tepidum at 0.72 angstrom resolution | ||||||
Components | High-potential iron-sulfur protein | ||||||
Keywords | ELECTRON TRANSPORT / IRON-SULFUR CLUSTER | ||||||
Function / homology | Function and homology information aerobic electron transport chain / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Thermochromatium tepidum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.72 Å | ||||||
Authors | Takeda, K. / Kusumoto, K. / Hirano, Y. / Miki, K. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2010 Title: Detailed assessment of X-ray induced structural perturbation in a crystalline state protein. Authors: Takeda, K. / Kusumoto, K. / Hirano, Y. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3a39.cif.gz | 72.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3a39.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 3a39.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a3/3a39 ftp://data.pdbj.org/pub/pdb/validation_reports/a3/3a39 | HTTPS FTP |
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-Related structure data
Related structure data | 3a38C 1iuaS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 8793.851 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Thermochromatium tepidum (bacteria) / References: UniProt: P80176 | ||||
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#2: Chemical | ChemComp-SF4 / | ||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | #5: 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: 1.82 Å3/Da / Density % sol: 32.6 % / Description: The file contains Friedel pairs. |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 Details: 1.9M ammonium sulfate, 10mM dithiothreitol, 100mM sodium citrate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.71 Å / Relative weight: 1 |
Reflection | Resolution: 0.72→50 Å / Num. obs: 157203 / % possible obs: 91.8 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 1.34 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 41.9 |
Reflection shell | Resolution: 0.72→0.74 Å / Redundancy: 3 % / Rmerge(I) obs: 0.194 / Mean I/σ(I) obs: 5.1 / Num. unique all: 3293 / % possible all: 54 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1IUA Resolution: 0.72→50 Å / Num. parameters: 8913 / Num. restraintsaints: 542 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER / Details: The file contains Friedel pairs.
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Refine analyze | Num. disordered residues: 31 / Occupancy sum hydrogen: 564.78 / Occupancy sum non hydrogen: 766.18 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.72→50 Å
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Refine LS restraints |
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