+Open data
-Basic information
Entry | Database: PDB / ID: 2zxy | ||||||
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Title | Crystal Structure of Cytochrome c555 from Aquifex aeolicus | ||||||
Components | Cytochrome c552 | ||||||
Keywords | OXYGEN BINDING / TRANSPORT PROTEIN / HEME PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Aquifex aeolicus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.15 Å | ||||||
Authors | Obuchi, M. / Kawahara, K. / Motooka, D. / Nakamura, S. / Yamanaka, M. / Takeda, T. / Uchiyama, S. / Kobayashi, Y. / Ohkubo, T. / Sambongi, Y. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2009 Title: Hyperstability and crystal structure of cytochrome c(555) from hyperthermophilic Aquifex aeolicus Authors: Obuchi, M. / Kawahara, K. / Motooka, D. / Nakamura, S. / Yamanaka, M. / Takeda, T. / Uchiyama, S. / Kobayashi, Y. / Ohkubo, T. / Sambongi, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zxy.cif.gz | 55.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zxy.ent.gz | 41.2 KB | Display | PDB format |
PDBx/mmJSON format | 2zxy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zx/2zxy ftp://data.pdbj.org/pub/pdb/validation_reports/zx/2zxy | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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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Details | AUTHOR STATES THAT THE BIOLOGICAL UNIT IS UNKNOWN |
-Components
#1: Protein | Mass: 9264.803 Da / Num. of mol.: 1 / Fragment: UNP residues 18-104 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: cycB2, aq_1550 / Plasmid: pKK223-3 / Production host: Escherichia coli (E. coli) / Strain (production host): RI90 / References: UniProt: O67504 |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 1.94 Å3/Da / Density % sol: 36.73 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 39% PEG 4000, 0.8M ammonium acetate, 0.1M tri-sodium citrate dehydrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation |
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Radiation wavelength |
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Reflection | Resolution: 1.15→50 Å / Num. obs: 25402 / % possible obs: 97 % / Redundancy: 3.71 % / Rmerge(I) obs: 0.047 | |||||||||||||||
Reflection shell | Resolution: 1.15→1.19 Å / Mean I/σ(I) obs: 10.01 / % possible all: 89.4 |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.15→15.92 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.959 / Cross valid method: THROUGHOUT / ESU R: 0.036 / ESU R Free: 0.038 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.536 Å2
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Refinement step | Cycle: LAST / Resolution: 1.15→15.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.153→1.183 Å / Total num. of bins used: 20
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