+Open data
-Basic information
Entry | Database: PDB / ID: 3cyr | |||||||||
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Title | CYTOCHROME C3 FROM DESULFOVIBRIO DESULFURICANS ATCC 27774P | |||||||||
Components | CYTOCHROME C3 | |||||||||
Keywords | ELECTRON TRANSPORT / CYTOCHROME | |||||||||
Function / homology | Function and homology information electron transfer activity / periplasmic space / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / RIGID-BODY REFINEMENT / Resolution: 1.6 Å | |||||||||
Authors | Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A. | |||||||||
Citation | Journal: Inorg.Chim.Acta. / Year: 1998 Title: Refinement of the Three-Dimensional Structures of Cytochrome C3 from Desulfovibrio Vulgaris Hildenborough at 1.67 Angstroms Resolution and from Desulfovibrio Desulfuricans Atcc 27774 at 1.6 Angstroms Resolution Authors: Simoes, P. / Matias, P.M. / Morais, J. / Wilson, K. / Dauter, Z. / Carrondo, M.A. #1: Journal: Biochemistry / Year: 1995 Title: Structure of the Tetraheme Cytochrome from Desulfovibrio Desulfuricans Atcc 27774: X-Ray Diffraction and Electron Paramagnetic Resonance Studies Authors: Morais, J. / Palma, P.N. / Frazao, C. / Caldeira, J. / Legall, J. / Moura, I. / Moura, J.J. / Carrondo, M.A. #2: Journal: Acta Crystallogr.,Sect.D / Year: 1994 Title: Crystallization and Preliminary X-Ray Diffraction Analysis of Tetra-Heme Cytochrome C3 from Sulfate-and Nitrate-Reducing Desulfovibrio Desulfuricans Atcc 27774 Authors: Frazao, C. / Morais, J. / Matias, P.M. / 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 | 3cyr.cif.gz | 36.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cyr.ent.gz | 28.1 KB | Display | PDB format |
PDBx/mmJSON format | 3cyr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/3cyr ftp://data.pdbj.org/pub/pdb/validation_reports/cy/3cyr | HTTPS FTP |
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-Related structure data
Related structure data | 2cyr 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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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 11589.472 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / References: UniProt: Q9L915 | ||
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#2: Chemical | ChemComp-HEM / #3: 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: 2.72 Å3/Da / Density % sol: 54.76 % |
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Crystal grow | pH: 4 Details: PROTEIN WAS CRYSTALLIZED FROM 3.5 M AMMONIUM SULFATE SOLUTION IN 0.05 M SODIUM ACETATE BUFFER (PH 4.0) |
Crystal grow | *PLUS Method: other / Details: Matias, P.M., (1993) J. Mol. Biol., 234, 680. |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.92 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1993 / Details: MIRROR |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→38.8 Å / Num. obs: 17593 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.7 |
Reflection shell | Resolution: 1.6→1.68 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.4 / % possible all: 98.4 |
Reflection | *PLUS Num. measured all: 88838 |
Reflection shell | *PLUS % possible obs: 98.4 % |
-Processing
Software |
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Refinement | Method to determine structure: RIGID-BODY REFINEMENT Starting model: PDB ENTRY 2CYR 2cyr Resolution: 1.6→8 Å / Num. parameters: 4263 / Num. restraintsaints: 10149 / Cross valid method: FREE R / σ(F): 1 / Details: X-PLOR USED INITIALLY
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Refine analyze | Num. disordered residues: 2 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→8 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-93 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Num. reflection obs: 16390 / Rfactor obs: 0.166 / Rfactor Rwork: 0.175 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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