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Yorodumi- PDB-1eyt: CRYSTAL STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THER... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1eyt | ||||||
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Title | CRYSTAL STRUCTURE OF HIGH-POTENTIAL IRON-SULFUR PROTEIN FROM THERMOCHROMATIUM TEPIDUM | ||||||
Components | HIGH-POTENTIAL IRON-SULFUR PROTEIN | ||||||
Keywords | ELECTRON TRANSPORT / Iron-sulfur protein | ||||||
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 / Resolution: 1.5 Å | ||||||
Authors | Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2000 Title: Crystal structures of photosynthetic reaction center and high-potential iron-sulfur protein from Thermochromatium tepidum: thermostability and electron transfer. Authors: Nogi, T. / Fathir, I. / Kobayashi, M. / Nozawa, T. / Miki, K. #1: Journal: Acta Crystallogr.,Sect.D / Year: 2000 Title: Crystallization and Preliminary Crystallographic Analysis of High-potential Iron-sulfur Protein from Thermochromatium tepidum Authors: Nogi, T. / Kobayashi, M. / Nozawa, T. / Miki, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1eyt.cif.gz | 28.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1eyt.ent.gz | 17.3 KB | Display | PDB format |
PDBx/mmJSON format | 1eyt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1eyt_validation.pdf.gz | 386 KB | Display | wwPDB validaton report |
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Full document | 1eyt_full_validation.pdf.gz | 387 KB | Display | |
Data in XML | 1eyt_validation.xml.gz | 3.2 KB | Display | |
Data in CIF | 1eyt_validation.cif.gz | 4.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ey/1eyt ftp://data.pdbj.org/pub/pdb/validation_reports/ey/1eyt | HTTPS FTP |
-Related 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: 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: 1.88 Å3/Da / Density % sol: 34.72 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.5 Details: ammonium sulfate, sodium citrate, pH 3.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 297 K / Method: vapor diffusionDetails: Nogi, T., (2000) Acta Crystallogr., Sect.D, 56, 656. | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 |
Detector | Type: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Nov 17, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→20 Å / Num. all: 10306 / Num. obs: 9746 / % possible obs: 86.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 8.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 1.5→1.53 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.219 / Num. unique all: 561 / % possible all: 67.6 |
Reflection | *PLUS Num. obs: 10306 / Num. measured all: 50767 |
Reflection shell | *PLUS % possible obs: 67.6 % / Mean I/σ(I) obs: 6 |
-Processing
Software |
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Refinement | Resolution: 1.5→10 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 1.57 Å / Rfactor Rfree: 0.248 / Rfactor Rwork: 0.247 |