+Open data
-Basic information
Entry | Database: PDB / ID: 1e3d | |||||||||
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Title | [NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774 | |||||||||
Components | ([NiFe] hydrogenase ...) x 2 | |||||||||
Keywords | HYDROGENASE / MOLECULAR MODELLING / ELECTRON TRANSFER | |||||||||
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 desulfuricans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | |||||||||
Authors | Matias, P.M. / Soares, C.M. / Saraiva, L.M. / Coelho, R. / Morais, J. / Le Gall, J. / Carrondo, M.A. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2001 Title: [Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with ...Title: [Nife] Hydrogenase from Desulfovibrio Desulfuricans Atcc 27774: Gene Sequencing, Three-Dimensional Structure Determination and Refinement at 1.8 A and Modelling Studies of its Interaction with the Tetrahaem Cytochrome C3. Authors: Matias, P.M. / Soares, C.M. / Saraiva, L.M. / Coelho, R. / Morais, J. / Le Gall, J. / Carrondo, M.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1e3d.cif.gz | 606.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1e3d.ent.gz | 502.4 KB | Display | PDB format |
PDBx/mmJSON format | 1e3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e3/1e3d ftp://data.pdbj.org/pub/pdb/validation_reports/e3/1e3d | 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-[NiFe] hydrogenase ... , 2 types, 4 molecules ACBD
#1: Protein | Mass: 28682.602 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: Q9L869 #2: Protein | Mass: 60009.902 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: Q9L868 |
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-Non-polymers , 7 types, 1413 molecules
#3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-H2S / #7: Chemical | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Details
Sequence details | THERE IS AN INITIAL MET 1 THAT WAS NOT CONSIDERED IN THE SEQUENCE USED FOR THE CRYSTALLOGRAPHIC ...THERE IS AN INITIAL MET 1 THAT WAS NOT CONSIDERED |
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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: 2.23 Å3/Da / Density % sol: 44.78 % | ||||||||||||||||||||||||||||||
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Crystal grow | pH: 8.5 Details: 25% (W/V) PEG 4000, 0.1 M TRIS-HCL BUFFER PH 8.5, 0.2 M MGCL2 AND A TRACE AMOUNT OF A DETERGENT, C12-DAO. | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, sitting drop | ||||||||||||||||||||||||||||||
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: ID14-4 / Wavelength: 0.932 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 15, 1999 / Details: TOROIDAL MIRROR |
Radiation | Monochromator: DOUBLE CRYSTAL SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.932 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→32 Å / Num. obs: 135264 / % possible obs: 95.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 4.5 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 1.7 / % possible all: 96 |
Reflection | *PLUS Num. measured all: 337524 |
Reflection shell | *PLUS % possible obs: 96 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FRV Resolution: 1.8→25 Å / Num. parameters: 55536 / Num. restraintsaints: 52359 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: FOR EACH CHAIN THE N-TERMINAL RESIDUES 1-4 (CHAINS A AND C) AND 1-5 (CHAINS B AND D) WERE NOT OBSERVED IN THE DENSITY MAPS
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Solvent computation | Solvent model: MOEWS & KRETSINGER | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 11896.01 / Occupancy sum non hydrogen: 13663.51 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rwork: 0.1671 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |