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Yorodumi- PDB-19hc: NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 -
+Open data
-Basic information
Entry | Database: PDB / ID: 19hc | ||||||
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Title | NINE-HAEM CYTOCHROME C FROM DESULFOVIBRIO DESULFURICANS ATCC 27774 | ||||||
Components | PROTEIN (NINE-HAEM CYTOCHROME C) | ||||||
Keywords | ELECTRON TRANSPORT / ELECTRON TRANSFER / CYTOCHROME | ||||||
Function / homology | Function and homology information periplasmic space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | ||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å | ||||||
Authors | Matias, P.M. / Coelho, R. / Pereira, I.A.C. / Coelho, A.V. / Thompson, A.W. / Sieker, L. / Gall, J.L. / Carrondo, M.A. | ||||||
Citation | Journal: Structure Fold.Des. / Year: 1999 Title: The primary and three-dimensional structures of a nine-haem cytochrome c from Desulfovibrio desulfuricans ATCC 27774 reveal a new member of the Hmc family. Authors: Matias, P.M. / Coelho, R. / Pereira, I.A. / Coelho, A.V. / Thompson, A.W. / Sieker, L.C. / Gall, J.L. / Carrondo, M.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 19hc.cif.gz | 244.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb19hc.ent.gz | 191.1 KB | Display | PDB format |
PDBx/mmJSON format | 19hc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 19hc_validation.pdf.gz | 6.5 MB | Display | wwPDB validaton report |
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Full document | 19hc_full_validation.pdf.gz | 6.5 MB | Display | |
Data in XML | 19hc_validation.xml.gz | 37.2 KB | Display | |
Data in CIF | 19hc_validation.cif.gz | 56.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/9h/19hc ftp://data.pdbj.org/pub/pdb/validation_reports/9h/19hc | HTTPS FTP |
-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
#1: Protein | Mass: 31290.666 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Desulfovibrio desulfuricans (bacteria) / Cellular location: PERIPLASMIC (PRESUMED) / References: UniProt: Q9RN68 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-HEM / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.42 Å3/Da / Density % sol: 64 % | |||||||||||||||
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Crystal grow | pH: 5.5 Details: PEG 6000 2-10% (W/V) SODIUM ACETATE BUFFER PH 5.5 0.25-0.75M | |||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: Coelho, A.V., (1996) Acta Crystallogr. D52, 1202. | |||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 110 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.7377, 1.7398, 1.7408, 0.8856 | |||||||||||||||
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 1, 1998 / Details: MIRRORS | |||||||||||||||
Radiation | Monochromator: SI (111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.8→24.2 Å / Num. obs: 91192 / % possible obs: 98.8 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 16.8 | |||||||||||||||
Reflection shell | Resolution: 1.8→1.87 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.116 / Mean I/σ(I) obs: 6.2 / % possible all: 93.1 | |||||||||||||||
Reflection | *PLUS Num. measured all: 425233 | |||||||||||||||
Reflection shell | *PLUS % possible obs: 93.1 % |
-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.8→24 Å / Num. parameters: 24762 / Num. restraintsaints: 24527 / Cross valid method: NONE IN LAST CYCLES / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: ANISOTROPIC SCALING APPLIED BY THE METHOD OF PARKIN, MOEZZI & HOPE, J.APPL.CRYST.28 (1995)53-56
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Solvent computation | Solvent model: MOEWS & KRETSINGER, J.MOL.BIOL.91(1973)201-228 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 14 / Occupancy sum non hydrogen: 5876.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→24 Å
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Refine LS restraints |
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