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Yorodumi- PDB-1hfe: 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hfe | ||||||
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Title | 1.6 A RESOLUTION STRUCTURE OF THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS | ||||||
Components | (PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) ...) x 2 | ||||||
Keywords | HYDROGENASE / FE-ONLY HYDROGENASE / HYDROGENE METABOLISM / PERIPLASM | ||||||
Function / homology | Function and homology information ferredoxin hydrogenase / ferredoxin hydrogenase activity / iron-sulfur cluster binding / 4 iron, 4 sulfur cluster binding / electron transfer activity / periplasmic space / iron ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.6 Å | ||||||
Authors | Nicolet, Y. / Piras, C. / Legrand, P. / Hatchikian, E.C. / Fontecilla-Camps, J.C. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: Desulfovibrio desulfuricans iron hydrogenase: the structure shows unusual coordination to an active site Fe binuclear center. Authors: Nicolet, Y. / Piras, C. / Legrand, P. / Hatchikian, C.E. / 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 | 1hfe.cif.gz | 238.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hfe.ent.gz | 185.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hfe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/1hfe ftp://data.pdbj.org/pub/pdb/validation_reports/hf/1hfe | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-PROTEIN (FE-ONLY HYDROGENASE (E.C.1.18.99.1) ... , 2 types, 4 molecules STLM
#1: Protein | Mass: 13646.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS HAS EXACTLY THE SAME SEQUENCE AS THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH) Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Cellular location: PERIPLASM / Species: Desulfovibrio vulgaris / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / References: UniProt: P07603, 1.18.99.1 #2: Protein | Mass: 46011.133 Da / Num. of mol.: 2 / Source method: isolated from a natural source Details: THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO DESULFURICANS HAS EXACTLY THE SAME SEQUENCE AS THE FE-ONLY HYDROGENASE FROM DESULFOVIBRIO VULGARIS (STRAIN HILDENBOROUGH) Source: (natural) Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough (bacteria) Cellular location: PERIPLASM / Species: Desulfovibrio vulgaris / Strain: Hildenborough / ATCC 29579 / NCIMB 8303 / References: UniProt: P07598, 1.18.99.1 |
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-Non-polymers , 8 types, 1202 molecules
#3: Chemical | ChemComp-ZN / | ||||||||||||
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#4: Chemical | ChemComp-FE2 / #5: Chemical | ChemComp-CYN / #6: Chemical | ChemComp-SF4 / #7: Chemical | #8: Chemical | ChemComp-CMO / #9: Chemical | #10: 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: 2.32 Å3/Da / Density % sol: 35 % | ||||||||||||||||||||||||
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Crystal grow | pH: 7.6 / Details: pH 7.60 | ||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop / pH: 5 | ||||||||||||||||||||||||
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: ID14-3 / Wavelength: 0.947375 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: May 1, 1998 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.947375 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→21 Å / Num. obs: 158363 / % possible obs: 94.3 % / Redundancy: 6.4 % / Biso Wilson estimate: 14.27 Å2 / Rsym value: 0.071 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.51→1.6 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.1 / Rsym value: 0.452 / % possible all: 89.2 |
Reflection | *PLUS Rmerge(I) obs: 0.071 |
Reflection shell | *PLUS % possible obs: 89.2 % / Rmerge(I) obs: 0.452 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.6→7 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE 2 MOLECULES OF THE ASYMMETRIC UNIT WERE NEVER CONSTRAINT WITH THE NON CRYSTALLOGRAPHIC SYMMETRY DURING REFINEMENT.
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Displacement parameters | Biso mean: 16.52 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.67 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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