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Yorodumi- PDB-1b4n: FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1b4n | ||||||
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Title | FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE FROM PYROCOCCUS FURIOSUS, COMPLEXED WITH GLUTARATE | ||||||
Components | FORMALDEHYDE FERREDOXIN OXIDOREDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / TUNGSTOENZYME / MOCO / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 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.J. / Dunn, D.M. / Weiss, R. / Adams, M.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1b4n.cif.gz | 476.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1b4n.ent.gz | 392.1 KB | Display | PDB format |
PDBx/mmJSON format | 1b4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1b4n_validation.pdf.gz | 686.9 KB | Display | wwPDB validaton report |
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Full document | 1b4n_full_validation.pdf.gz | 743.3 KB | Display | |
Data in XML | 1b4n_validation.xml.gz | 53.5 KB | Display | |
Data in CIF | 1b4n_validation.cif.gz | 78.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b4/1b4n ftp://data.pdbj.org/pub/pdb/validation_reports/b4/1b4n | HTTPS FTP |
-Related structure data
Related structure data | 1b25C 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
-Protein , 1 types, 4 molecules ABCD
#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 |
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-Non-polymers , 5 types, 200 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-SF4 / #4: Chemical | ChemComp-GUA / #5: Chemical | ChemComp-PTE / #6: 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: 56.17 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Apr 1, 1997 |
Radiation | Monochromator: MIRRORS / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. obs: 93705 / % possible obs: 77.6 % / Observed criterion σ(I): 0 / Redundancy: 2.1 % / Biso Wilson estimate: 32 Å2 / Rsym value: 0.059 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.158 / % possible all: 40.3 |
Reflection | *PLUS Num. measured all: 193320 / Rmerge(I) obs: 0.059 |
Reflection shell | *PLUS % possible obs: 40.3 % / Rmerge(I) obs: 0.158 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AOR Resolution: 2.4→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 23.8 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati d res low obs: 0 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→30 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.51 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rwork: 0.27 |