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Yorodumi- PDB-3daf: The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3daf | ||||||
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Title | The crystal structure of [Fe]-hydrogenase holoenzyme (HMD) from METHANOCALDOCOCCUS JANNASCHII cocrystallized with cyanide | ||||||
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 | 3daf.cif.gz | 87.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3daf.ent.gz | 63.8 KB | Display | PDB format |
PDBx/mmJSON format | 3daf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3daf_validation.pdf.gz | 778.4 KB | Display | wwPDB validaton report |
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Full document | 3daf_full_validation.pdf.gz | 781.3 KB | Display | |
Data in XML | 3daf_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 3daf_validation.cif.gz | 25.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/da/3daf ftp://data.pdbj.org/pub/pdb/validation_reports/da/3daf | HTTPS FTP |
-Related structure data
Related structure data | 3dagC 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
-Protein , 1 types, 1 molecules A
#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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-Non-polymers , 6 types, 220 molecules
#2: Chemical | ChemComp-PO4 / | ||||
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#3: Chemical | ChemComp-FE2 / | ||||
#4: Chemical | ChemComp-CYN / | ||||
#5: Chemical | #6: Chemical | ChemComp-FEG / | #7: 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: 2.64 Å3/Da / Density % sol: 53.42 % |
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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, cyanide, 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: 1.75→30 Å / Num. all: 36729 / Num. obs: 36729 / % possible obs: 0.901 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.065 / Rsym value: 0.065 / Net I/σ(I): 18.3 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 4 / Num. unique all: 2389 / Rsym value: 0.51 / % possible all: 73.1 |
-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: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.094 / SU ML: 0.076 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.114 / ESU R Free: 0.112 / 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: 34.124 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: 21.241 Å / Origin y: 5.136 Å / Origin z: 19.481 Å
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Refinement TLS group |
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