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Yorodumi- PDB-1frf: CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRU... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1frf | ||||||||||||
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Title | CRYSTAL STRUCTURE OF THE NI-FE HYDROGENASE FROM DESULFOVIBRIO FRUCTOSOVORANS | ||||||||||||
Components | ([NI-FE] HYDROGENASE) x 2 | ||||||||||||
Keywords | OXIDOREDUCTASE / NI-FE HYDROGENASE | ||||||||||||
Function / homology | Function and homology information cytochrome-c3 hydrogenase / cytochrome-c3 hydrogenase activity / ferredoxin hydrogenase complex / ferredoxin hydrogenase activity / 3 iron, 4 sulfur cluster binding / nickel cation binding / 4 iron, 4 sulfur cluster binding / periplasmic space / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Desulfovibrio fructosovorans (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | ||||||||||||
Authors | Montet, Y. / Volbeda, A. / Piras, C. / Hatchikian, E.C. / Frey, M. / Fontecilla, J.C. | ||||||||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 1998 Title: 3Fe-4S] to [4Fe-4S] cluster conversion in Desulfovibrio fructosovorans [NiFe] hydrogenase by site-directed mutagenesis Authors: Rousset, M. / Montet, Y. / Guigliarelli, B. / Forget, N. / Asso, M. / Bertrand, P. / Fontecilla-Camps, J.C. / Hatchikian, E.C. #1: Journal: Nat.Struct.Biol. / Year: 1997 Title: Gas Access to the Active Site of Ni-Fe Hydrogeases Probed by X-Ray Crystallography and Molecular Dynamics Authors: Montet, Y. / Amara, P. / Volbeda, A. / Vernede, X. / Hatchikian, E.C. / Field, M.J. / Frey, M. / Fontecilla-Camps, J.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1frf.cif.gz | 171.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1frf.ent.gz | 132.8 KB | Display | PDB format |
PDBx/mmJSON format | 1frf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fr/1frf ftp://data.pdbj.org/pub/pdb/validation_reports/fr/1frf | HTTPS FTP |
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-Related structure data
Related structure data | 1frvS S: Starting model for refinement |
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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: (Code: given Matrix: (0.394555, 0.745792, 0.536769), Vector: |
-Components
-Protein , 2 types, 2 molecules SL
#1: Protein | [ Mass: 28422.400 Da / Num. of mol.: 1 / Fragment: SMALL CHAIN / Source method: isolated from a natural source / Details: DSM 3604 / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P18187, 1.18.99.1 |
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#2: Protein | [ Mass: 61669.488 Da / Num. of mol.: 1 / Fragment: LARGE CHAIN / Source method: isolated from a natural source / Details: DSM 3604 / Source: (natural) Desulfovibrio fructosovorans (bacteria) / Cellular location: PERIPLASM / Strain: WILD TYPE / References: UniProt: P18188, 1.18.99.1 |
-Non-polymers , 6 types, 138 molecules
#3: Chemical | #4: Chemical | ChemComp-F3S / | #5: Chemical | ChemComp-FE / | #6: Chemical | ChemComp-NI / | #7: Chemical | ChemComp-MG / | #8: 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: 2.2 Å3/Da / Density % sol: 44.1 % | |||||||||||||||||||||||||
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Crystal grow | pH: 6.4 Details: PEG 6000 28%, MES 100MM PH 6,4 25MM OCTYL-BETA-D-GLUCOPYRANOSIDE, pH 6.4 | |||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM02 / Wavelength: 0.9794 |
Detector | Date: Oct 1, 1996 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9794 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→38.7 Å / Num. obs: 43607 / % possible obs: 66.7 % / Observed criterion σ(I): 2 / Redundancy: 2.8 % / Rsym value: 0.061 / Net I/σ(I): 10.2 |
Reflection shell | Resolution: 2.7→2.77 Å / Redundancy: 1.3 % / Mean I/σ(I) obs: 2 / Rsym value: 0.32 / % possible all: 56.4 |
Reflection | *PLUS Num. obs: 33794 / % possible obs: 74 % / Num. measured all: 79013 / Rmerge(I) obs: 0.077 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1FRV Resolution: 2.7→12 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0.001 / σ(F): 2 Details: THERE ARE THREE MOLECULES PER ASYMETRIC UNIT. IN ALL REFINEMENT STEPS, THE STRICT NON CRYSTALLOGRAPHIC SYMMETRY WAS USED. THERE IS NO ELECTRON DENSITY FOR RESIDUES 1 - 5 OF THE LARGE SUBUNIT ...Details: THERE ARE THREE MOLECULES PER ASYMETRIC UNIT. IN ALL REFINEMENT STEPS, THE STRICT NON CRYSTALLOGRAPHIC SYMMETRY WAS USED. THERE IS NO ELECTRON DENSITY FOR RESIDUES 1 - 5 OF THE LARGE SUBUNIT AND RESIDUES 1 - 3 FOR THE SMALL ONE. SOME ATOMS HAVE OCCUPANCIES LESS THAN 1.0 : THEY BELONG TO LATERAL CHAINS WHICH ARE DISORDERED , AS THEY ARE LOCATED ON THE SURFACE OF THE PROTEIN.
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Displacement parameters | Biso mean: 12.48 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→12 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: STRICT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 12 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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