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Yorodumi- PDB-1aqe: CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1aqe | ||||||
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Title | CRYSTAL STRUCTURE OF THE Y73E MUTANT OF CYTOCHROME C OF CLASS III (AMBLER) 26 KD | ||||||
Components | CYTOCHROME C3 | ||||||
Keywords | ELECTRON TRANSPORT / OCTAHEME CYTOCHROME / POINT MUTANT | ||||||
Function / homology | Function and homology information anaerobic respiration / periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfomicrobium norvegicum (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Czjzek, M. / Haser, R. | ||||||
Citation | Journal: Biochemistry / Year: 1998 Title: Structural and kinetic studies of the Y73E mutant of octaheme cytochrome c3 (Mr = 26 000) from Desulfovibrio desulfuricans Norway. Authors: Aubert, C. / Giudici-Orticoni, M.T. / Czjzek, M. / Haser, R. / Bruschi, M. / Dolla, A. #1: Journal: J.Biol.Chem. / Year: 1997 Title: A Single Mutation in the Heme 4 Environment of Desulfovibrio Desulfuricans Norway Cytochrome C3 (Mr 26,000) Greatly Affects the Molecule Reactivity Authors: Aubert, C. / Leroy, G. / Bruschi, M. / Wall, J.D. / Dolla, A. #2: Journal: Structure / Year: 1996 Title: Crystal Structure of a Dimeric Octaheme Cytochrome C3 (Mr 26,000) from Desulfovibrio Desulfuricans Norway Authors: Czjzek, M. / Guerlesquin, F. / Bruschi, M. / Haser, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1aqe.cif.gz | 46.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1aqe.ent.gz | 37.1 KB | Display | PDB format |
PDBx/mmJSON format | 1aqe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1aqe_validation.pdf.gz | 1.6 MB | Display | wwPDB validaton report |
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Full document | 1aqe_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 1aqe_validation.xml.gz | 8.2 KB | Display | |
Data in CIF | 1aqe_validation.cif.gz | 10.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/1aqe ftp://data.pdbj.org/pub/pdb/validation_reports/aq/1aqe | HTTPS FTP |
-Related structure data
Related structure data | 1czjS 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
#1: Protein | Mass: 12506.900 Da / Num. of mol.: 1 / Mutation: Y73E Source method: isolated from a genetically manipulated source Details: MR 26000 / Source: (gene. exp.) Desulfomicrobium norvegicum (bacteria) / Strain: Norway 4 Description: SULFATE REDUCING BACTERIA, ALSO KNOWN AS DESULFOMICROBIUM BACULATUM Plasmid: PJRD215 / Production host: Desulfovibrio desulfuricans (bacteria) / References: UniProt: P38554 | ||
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#2: Chemical | ChemComp-SO4 / | ||
#3: Chemical | ChemComp-HEM / #4: 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: 3.53 Å3/Da / Density % sol: 65 % | |||||||||||||||||||||||||
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Crystal grow | pH: 7.6 Details: THE PROTEIN WAS CRYSTALLIZED FROM 2.4M AMMONIUM SULFATE, 100MM TRIS PH 7.6 | |||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Czjzek, M., (1992) J. Mol. Biol., 228, 995. | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 20, 1997 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→25 Å / Num. obs: 9880 / % possible obs: 95.7 % / Observed criterion σ(I): 1 / Redundancy: 5.2 % / Biso Wilson estimate: 20.97 Å2 / Rmerge(I) obs: 0.096 |
Reflection shell | Resolution: 2.2→2.25 Å / Redundancy: 4 % / Rmerge(I) obs: 0.35 / % possible all: 91.1 |
Reflection | *PLUS Num. measured all: 53789 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CZJ Resolution: 2.2→22 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 1
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Displacement parameters | Biso mean: 21.32 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.3 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.843 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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