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Yorodumi- PDB-1c75: 0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BAC... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c75 | ||||||||||||
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Title | 0.97 A "AB INITIO" CRYSTAL STRUCTURE OF CYTOCHROME C-553 FROM BACILLUS PASTEURII | ||||||||||||
Components | CYTOCHROME C-553 | ||||||||||||
Keywords | ELECTRON TRANSPORT / C-553 / HEME / CYTOCHROME / BACILLUS PASTEURII / AB INITIO / ATOMIC RESOLUTION | ||||||||||||
Function / homology | Function and homology information electron transfer activity / iron ion binding / heme binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Sporosarcina pasteurii (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 0.97 Å | ||||||||||||
Authors | Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. | ||||||||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Crystal structure of oxidized Bacillus pasteurii cytochrome c553 at 0.97-A resolution. Authors: Benini, S. / Gonzalez, A. / Rypniewski, W.R. / Wilson, K.S. / Van Beeumen, J.J. / Ciurli, S. #1: Journal: Biochem.Biophys.Res.Commun. / Year: 1999 Title: Cytochrome C-553 from the Alkalophilic Bacterium Bacillus Pasteurii Has the Primary Structure Characteristics of a Lipoprotein Authors: Vandenberghe, I.H.M. / Guisez, Y. / Ciurli, S. / Benini, S. / Van-Beeumen, J.J. #2: Journal: J.Biol.Inorg.Chem. / Year: 1998 Title: Modulation of Bacillus Pasteurii Cytochrome C553 Reduction Potential by Structural and Solution Parameters Authors: Benini, S. / Borsari, M. / Ciurli, S. / Dikiy, A. / Lamborghini, M. #3: Journal: Proteins / Year: 1997 Title: Crystals of Cytochrome C-553 from Bacillus Pasteurii Show Diffraction to 0.97 A Resolution Authors: Benini, S. / Ciurli, S. / Rypniewski, W.R. / Wilson, K.S. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c75.cif.gz | 64.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c75.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 1c75.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c7/1c75 ftp://data.pdbj.org/pub/pdb/validation_reports/c7/1c75 | HTTPS FTP |
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-Related 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: 7115.937 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: DEUTSCHE SAMMLUNG VON MIKROORGANISMEN (DSM) / Source: (natural) Sporosarcina pasteurii (bacteria) / Cellular location: CYTOPLASM / Strain: DSM 33 / References: UniProt: P82599 |
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#2: Chemical | ChemComp-HEC / |
#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: 2.08 Å3/Da / Density % sol: 38 % / Description: THE STRUCTURE WAS SOLVED "AB INITIO" | |||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: 3.2 M AMMONIUM SULPHATE IN 100 MM SODIUM CITRATE BUFFER PH 5.0 | |||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 41 % | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / pH: 8 / Method: vapor diffusion, hanging 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: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.885 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 23, 1996 / Details: SEGMENTED MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.885 Å / Relative weight: 1 |
Reflection | Resolution: 0.97→20 Å / Num. obs: 38959 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5.46 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 17.16 |
Reflection shell | Resolution: 0.97→0.99 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 4.18 / Rsym value: 0.242 / % possible all: 99.6 |
Reflection | *PLUS Lowest resolution: 20 Å / Redundancy: 5.47 % / Num. measured all: 212694 / Rmerge(I) obs: 0.074 |
Reflection shell | *PLUS |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 0.97→20 Å / Num. parameters: 6286 / Num. restraintsaints: 7877 / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 14 / Occupancy sum hydrogen: 486 / Occupancy sum non hydrogen: 661.12 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.97→20 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 5 % | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.7 Å2 | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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