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Yorodumi- PDB-1h98: New Insights into Thermostability of Bacterial Ferredoxins: High ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1h98 | ||||||
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Title | New Insights into Thermostability of Bacterial Ferredoxins: High Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus thermophilus | ||||||
Components | FERREDOXIN | ||||||
Keywords | ELECTRON TRANSPORT / THERMOPHILIC / IRON-SULFUR / AZOTOBACTER / HYDROGEN BONDS / STABILITY / HIGH RESOLUTION | ||||||
Function / homology | Function and homology information 3 iron, 4 sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | THERMUS AQUATICUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.64 Å | ||||||
Authors | Macedo-Ribeiro, S. / Martins, B.M. / Pereira, P.J.B. / Buse, G. / Huber, R. / Soulimane, T. | ||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2001 Title: New Insights Into the Thermostability of Bacterial Ferredoxins: High-Resolution Crystal Structure of the Seven-Iron Ferredoxin from Thermus Thermophilus Authors: Macedo-Ribeiro, S. / Martins, B.M. / Pereira, P.J.B. / Buse, G. / Huber, R. / Soulimane, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1h98.cif.gz | 29.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1h98.ent.gz | 18.6 KB | Display | PDB format |
PDBx/mmJSON format | 1h98.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1h98_validation.pdf.gz | 375.6 KB | Display | wwPDB validaton report |
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Full document | 1h98_full_validation.pdf.gz | 375.5 KB | Display | |
Data in XML | 1h98_validation.xml.gz | 2.8 KB | Display | |
Data in CIF | 1h98_validation.cif.gz | 4.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/1h98 ftp://data.pdbj.org/pub/pdb/validation_reports/h9/1h98 | HTTPS FTP |
-Related structure data
Related structure data | 6fd1S 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: 8693.865 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) THERMUS AQUATICUS (bacteria) / References: UniProt: P03942 |
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#2: Chemical | ChemComp-SF4 / |
#3: Chemical | ChemComp-F3S / |
#4: Water | ChemComp-HOH / |
Compound details | TRANSFER ELECTRONS IN A WIDE VARIETY OF METABOLIC REACTIONS |
Sequence details | LEU 69 A GLY 97 ARE COVALENTLY LINKED. THE RESIDUES 70 TO 96 FROM SWISSPROT ENTRY P03942 ARE NOT ...LEU 69 A GLY 97 ARE COVALENTLY |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 46 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.4 Details: 2.2 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE PH 5.0-5.4, 5-10% GLYCEROL | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7 / Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.64→13.4 Å / Num. obs: 9579 / % possible obs: 96.3 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 5 |
Reflection shell | Resolution: 1.64→1.73 Å / Rmerge(I) obs: 0.234 / Mean I/σ(I) obs: 2.4 / % possible all: 98.8 |
Reflection | *PLUS Lowest resolution: 13.4 Å / Num. measured all: 183792 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6FD1 Resolution: 1.64→8 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 19.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.64→8 Å
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Refine LS restraints |
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Xplor file |
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Refinement | *PLUS Lowest resolution: 8 Å / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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