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Yorodumi- PDB-3dag: The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3dag | ||||||
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Title | The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII | ||||||
Components | 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||
Keywords | OXIDOREDUCTASE / ROSSMANN FOLD / HELIX BUNDLE / Methanogenesis / One-carbon metabolism | ||||||
Function / homology | Function and homology information 5,10-methenyltetrahydromethanopterin hydrogenase / N5,N10-methenyltetrahydromethanopterin hydrogenase activity / methanogenesis, from carbon dioxide / pyrroline-5-carboxylate reductase activity / L-proline biosynthetic process / one-carbon metabolic process Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Pilak, O. / Warkentin, E. / Shima, S. / Thauer, R.K. / Ermler, U. | ||||||
Citation | Journal: Science / Year: 2008 Title: The crystal structure of [Fe]-hydrogenase reveals the geometry of the active site. Authors: Shima, S. / Pilak, O. / Vogt, S. / Schick, M. / Stagni, M.S. / Meyer-Klaucke, W. / Warkentin, E. / Thauer, R.K. / Ermler, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3dag.cif.gz | 86.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3dag.ent.gz | 63.9 KB | Display | PDB format |
PDBx/mmJSON format | 3dag.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3dag ftp://data.pdbj.org/pub/pdb/validation_reports/da/3dag | HTTPS FTP |
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-Related structure data
Related structure data | 3dafC 2bojS 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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-Components
#1: Protein | Mass: 38709.016 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Strain: DSMZ2661 / Gene: hmd, MJ0784 / Plasmid: PET24B / Production host: Escherichia coli (E. coli) / Strain (production host): B834 (DE3)(PLYSS) References: UniProt: Q58194, 5,10-methenyltetrahydromethanopterin hydrogenase | ||
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#2: Chemical | ChemComp-FE2 / | ||
#3: Chemical | ChemComp-FEG / | ||
#4: Chemical | #5: 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: 2.57 Å3/Da / Density % sol: 52.17 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50% MPD, 0.1M TRIS/HCL, 20mM NH4H2PO4, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99198 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: mirrors |
Radiation | Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99198 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. all: 35596 / Num. obs: 35596 / % possible obs: 0.904 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.067 / Rsym value: 0.055 / Net I/σ(I): 16.92 |
Reflection shell | Resolution: 1.7→1.8 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3 / % possible all: 0.71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2BOJ Resolution: 1.75→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.32 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.601 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.794 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 21.0611 Å / Origin y: 4.9788 Å / Origin z: 19.4654 Å
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Refinement TLS group |
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