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- PDB-3f47: The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from M... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3f47 | ||||||
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Title | The Crystal Structure of [Fe]-Hydrogenase (Hmd) Holoenzyme from Methanocaldococcus jannaschii | ||||||
![]() | 5,10-methenyltetrahydromethanopterin hydrogenase | ||||||
![]() | OXIDOREDUCTASE / ROSSMANN FOLD / HELIX BUNDLE / COMPLEX WITH IRON GUANYLYL PYRIDINOL COFACTOR / Methanogenesis / One-carbon metabolism | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hiromoto, T. / Pilak, O. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U. | ||||||
![]() | ![]() Title: The crystal structure of C176A mutated [Fe]-hydrogenase suggests an acyl-iron ligation in the active site iron complex. Authors: Hiromoto, T. / Ataka, K. / Pilak, O. / Vogt, S. / Stagni, M.S. / Meyer-Klaucke, W. / Warkentin, E. / Thauer, R.K. / Shima, S. / Ermler, U. #1: ![]() 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. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 90.2 KB | Display | ![]() |
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PDB format | ![]() | 66.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 792.4 KB | Display | ![]() |
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Full document | ![]() | 795.8 KB | Display | |
Data in XML | ![]() | 16.9 KB | Display | |
Data in CIF | ![]() | 25.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f46C ![]() 3dagS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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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: 38739.066 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: DSM 2661 / Gene: hmd, MJ0784 / Plasmid: pET-24b(+) / Production host: ![]() ![]() References: UniProt: Q58194, 5,10-methenyltetrahydromethanopterin hydrogenase |
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-Non-polymers , 5 types, 243 molecules ![](data/chem/img/I2C.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/CMO.gif)
![](data/chem/img/NA.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-I2C / | ||||
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#3: Chemical | ChemComp-FE2 / | ||||
#4: Chemical | #5: Chemical | ChemComp-NA / | #6: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50.04 % |
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Crystal grow | Temperature: 283 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 50% MPD, 100mM Tris-HCl, 20mM Ammonium dihydrogen phosphate, 1mM DTT , pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 283K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 1, 2007 / Details: Dynamically bendable mirror |
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.992 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→26.2 Å / Num. obs: 37583 / % possible obs: 95.5 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Biso Wilson estimate: 32.677 Å2 / Rmerge(I) obs: 0.056 / Net I/σ(I): 16 |
Reflection shell | Resolution: 1.75→1.8 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 2.6 / Num. measured obs: 9296 / Num. unique all: 9296 / Num. unique obs: 2563 / % possible all: 81.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3DAG Resolution: 1.75→25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.959 / WRfactor Rfree: 0.215 / WRfactor Rwork: 0.179 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.862 / SU B: 4.613 / SU ML: 0.074 / SU R Cruickshank DPI: 0.111 / SU Rfree: 0.107 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.111 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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 max: 62.58 Å2 / Biso mean: 33.553 Å2 / Biso min: 21.27 Å2
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Refine analyze | Luzzati coordinate error obs: 0.243 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→25 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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