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Yorodumi- PDB-1dt1: THERMUS THERMOPHILUS CYTOCHROME C552 SYNTHESIZED BY ESCHERICHIA COLI -
+Open data
-Basic information
Entry | Database: PDB / ID: 1dt1 | |||||||||
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Title | THERMUS THERMOPHILUS CYTOCHROME C552 SYNTHESIZED BY ESCHERICHIA COLI | |||||||||
Components | CYTOCHROME C552 | |||||||||
Keywords | OXIDOREDUCTASE / Cytochrome C552 / Thermus thermophilus | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Fee, J.A. / Chen, Y. / Hill, M.J. / Gomez-Moran, E. / Loehr, T. / Ai, J. / Thony-Meyer, L. / Williams, P.A. / Stura, E. / Sridhar, V. / McRee, D.E. | |||||||||
Citation | Journal: Protein Sci. / Year: 2000 Title: Integrity of thermus thermophilus cytochrome c552 synthesized by Escherichia coli cells expressing the host-specific cytochrome c maturation genes, ccmABCDEFGH: biochemical, spectral, and ...Title: Integrity of thermus thermophilus cytochrome c552 synthesized by Escherichia coli cells expressing the host-specific cytochrome c maturation genes, ccmABCDEFGH: biochemical, spectral, and structural characterization of the recombinant protein. Authors: Fee, J.A. / Chen, Y. / Todaro, T.R. / Bren, K.L. / Patel, K.M. / Hill, M.G. / Gomez-Moran, E. / Loehr, T.M. / Ai, J. / Thony-Meyer, L. / Williams, P.A. / Stura, E. / Sridhar, V. / McRee, D.E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dt1.cif.gz | 36.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dt1.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 1dt1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dt/1dt1 ftp://data.pdbj.org/pub/pdb/validation_reports/dt/1dt1 | 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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Details | The biological unit is a monomer as found in the asymmetric unit |
-Components
#1: Protein | Mass: 13995.368 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SME3 |
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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: 2.48 Å3/Da / Density % sol: 50.4 % | ||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 36% MPEG 5K (w/v), 0.2M Im-mat 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 24K | ||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 8 | ||||||||||||||||||||||||||||||||||||
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: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 14, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.08 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→25 Å / Num. all: 92080 / Num. obs: 15100 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 14.9 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.1 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 3 % / Rmerge(I) obs: 0.304 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 92080 |
Reflection shell | *PLUS % possible obs: 98.8 % |
-Processing
Software |
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Refinement | Resolution: 1.8→25 Å / σ(F): 2 / σ(I): 4 / Stereochemistry target values: engh and huber
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Refinement step | Cycle: LAST / Resolution: 1.8→25 Å
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | ||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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