+Open data
-Basic information
Entry | Database: PDB / ID: 1b25 | ||||||
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Title | FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS | ||||||
Components | PROTEIN (FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE / MOCO / TUNGSTOENZYME / TUNGSTEN CONTAINING PROTEIN / HYPERTHERMOPHILE | ||||||
Function / homology | Function and homology information aldehyde ferredoxin oxidoreductase activity / aldehyde ferredoxin oxidoreductase / 4 iron, 4 sulfur cluster binding / electron transfer activity / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å | ||||||
Authors | Hu, Y.L. / Faham, S. / Roy, R. / Adams, M.W.W. / Rees, D.C. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Formaldehyde ferredoxin oxidoreductase from Pyrococcus furiosus: the 1.85 A resolution crystal structure and its mechanistic implications. Authors: Hu, Y. / Faham, S. / Roy, R. / Adams, M.W. / Rees, D.C. #1: Journal: J.Bacteriol. / Year: 1999 Title: Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus Furiosus: The Third of a Putative ...Title: Purification and Molecular Characterization of the Tungsten-Containing Formaldehyde Ferredoxin Oxidoreductase from the Hyperthermophilic Archaeon Pyrococcus Furiosus: The Third of a Putative Five Member Tungstoenzyme Family Authors: Roy, R. / Mukund, S. / Schut, G. / Dunn, D.M. / Weiss, R. / Adams, M.W.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b25.cif.gz | 504.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b25.ent.gz | 412.8 KB | Display | PDB format |
PDBx/mmJSON format | 1b25.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b25_validation.pdf.gz | 702.1 KB | Display | wwPDB validaton report |
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Full document | 1b25_full_validation.pdf.gz | 729.4 KB | Display | |
Data in XML | 1b25_validation.xml.gz | 49 KB | Display | |
Data in CIF | 1b25_validation.cif.gz | 81.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b2/1b25 ftp://data.pdbj.org/pub/pdb/validation_reports/b2/1b25 | HTTPS FTP |
-Related structure data
Related structure data | 1b4nC 1aorS S: Starting model for refinement C: citing same article (ref.) |
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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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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 68860.742 Da / Num. of mol.: 4 Fragment: DOMAIN 1: 1-208, DOMAIN 2: 209-406, DOMAIN 3: 407-619 Source method: isolated from a natural source / Source: (natural) Pyrococcus furiosus (archaea) / References: UniProt: O93738, UniProt: Q8U1K3*PLUS #2: Chemical | ChemComp-SF4 / #3: Chemical | ChemComp-PTT / #4: 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: 2.9 Å3/Da / Density % sol: 56.22 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.6 / Details: pH 5.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: melting-point capillary method | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 |
Detector | Detector: IMAGE PLATE / Date: Apr 1, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→20 Å / Num. obs: 240510 / % possible obs: 91.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.074 / Net I/σ(I): 14 |
Reflection shell | Resolution: 1.85→1.88 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.234 / % possible all: 83.6 |
Reflection | *PLUS Num. measured all: 928734 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS % possible obs: 83.6 % / Rmerge(I) obs: 0.234 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AOR Resolution: 1.85→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 17.1 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: UNRESTRAINED | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.85→1.93 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.174 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.256 |