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Yorodumi- PDB-1qv9: Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrog... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1qv9 | ||||||
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Title | Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: A methanogenic enzyme with an unusual quarternary structure | ||||||
Components | F420-dependent methylenetetrahydromethanopterin dehydrogenase | ||||||
Keywords | OXIDOREDUCTASE / monomer: alpha/beta domain / helix bundle / trimer of dimers | ||||||
Function / homology | Function and homology information methylenetetrahydromethanopterin dehydrogenase / methylenetetrahydromethanopterin dehydrogenase activity / methanogenesis, from carbon dioxide / ferredoxin hydrogenase activity / one-carbon metabolic process Similarity search - Function | ||||||
Biological species | Methanopyrus kandleri (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.54 Å | ||||||
Authors | Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Bourenkov, G. / Bartunik, H.D. / Ermler, U. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2003 Title: Coenzyme F420-dependent methylenetetrahydromethanopterin dehydrogenase (Mtd) from Methanopyrus kandleri: a methanogenic enzyme with an unusual quarternary structure Authors: Hagemeier, C.H. / Shima, S. / Thauer, R.K. / Bourenkov, G. / Bartunik, H.D. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qv9.cif.gz | 183.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qv9.ent.gz | 157 KB | Display | PDB format |
PDBx/mmJSON format | 1qv9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qv9_validation.pdf.gz | 451.4 KB | Display | wwPDB validaton report |
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Full document | 1qv9_full_validation.pdf.gz | 466.1 KB | Display | |
Data in XML | 1qv9_validation.xml.gz | 38 KB | Display | |
Data in CIF | 1qv9_validation.cif.gz | 55.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/1qv9 ftp://data.pdbj.org/pub/pdb/validation_reports/qv/1qv9 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 32213.100 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanopyrus kandleri (archaea) / Gene: MTD OR MK0011 / Production host: Escherichia coli (E. coli) / References: UniProt: P94951, EC: 1.5.99.9 #2: Chemical | ChemComp-MG / #3: 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: 2.58 Å3/Da / Density % sol: 52.37 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Mops/KOH, MPD, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
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: ESRF / Beamline: ID14-4 / Wavelength: 0.979 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 11, 2002 |
Radiation | Monochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.54→20 Å / Num. all: 145808 / Num. obs: 145808 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 21.4 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.55→1.62 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 3.9 / Num. unique all: 15700 / % possible all: 99.9 |
Reflection | *PLUS Highest resolution: 1.6 Å |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.54→19.92 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 5165889.15 / Data cutoff high rms absF: 5165889.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 51.0075 Å2 / ksol: 0.406286 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.54→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.54→1.64 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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