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Yorodumi- PDB-7ead: Crystal structure of beta-sheet cytochrome c prime from Thermus t... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7ead | ||||||||||||
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Title | Crystal structure of beta-sheet cytochrome c prime from Thermus thermophilus. | ||||||||||||
Components | Cytochrome_P460 domain-containing protein | ||||||||||||
Keywords | ELECTRON TRANSPORT / Cytochrome c / thermophile | ||||||||||||
Function / homology | HEME C / : Function and homology information | ||||||||||||
Biological species | Thermus thermophilus (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 Å | ||||||||||||
Authors | Yoshimi, T. / Fujii, S. / Oki, H. / Igawa, T. / Adams, R.H. / Ueda, K. / Kawahara, K. / Ohkubo, T. / Hough, A.M. / Sambongi, Y. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2022 Title: Crystal structure of thermally stable homodimeric cytochrome c'-beta from Thermus thermophilus. Authors: Yoshimi, T. / Fujii, S. / Oki, H. / Igawa, T. / Adams, H.R. / Ueda, K. / Kawahara, K. / Ohkubo, T. / Hough, M.A. / Sambongi, Y. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ead.cif.gz | 46.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7ead.ent.gz | 29.4 KB | Display | PDB format |
PDBx/mmJSON format | 7ead.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ead_validation.pdf.gz | 820.4 KB | Display | wwPDB validaton report |
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Full document | 7ead_full_validation.pdf.gz | 820.5 KB | Display | |
Data in XML | 7ead_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | 7ead_validation.cif.gz | 11.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ea/7ead ftp://data.pdbj.org/pub/pdb/validation_reports/ea/7ead | HTTPS FTP |
-Related structure data
Related structure data | 6hihS 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: 14942.125 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: TthHC11_22770 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A510IM14 |
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#2: Chemical | ChemComp-HEC / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.17 Å3/Da / Density % sol: 43.36 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop Details: 0.1 M 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid buffer (pH 7.5) and 20% (w/v) polyethylene glycol 10,000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Jul 17, 2019 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.74→41.15 Å / Num. obs: 13755 / % possible obs: 100 % / Redundancy: 13 % / Biso Wilson estimate: 16.98 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.197 / Net I/σ(I): 11.3 / Num. measured all: 178741 / Scaling rejects: 23 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6HIH Resolution: 1.74→36.42 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.88 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 54.19 Å2 / Biso mean: 22.4242 Å2 / Biso min: 12.24 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.74→36.42 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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