+Open data
-Basic information
Entry | Database: PDB / ID: 1duw | |||||||||
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Title | STRUCTURE OF NONAHEME CYTOCHROME C | |||||||||
Components | NONAHEME CYTOCHROME C | |||||||||
Keywords | ELECTRON TRANSPORT / heme / cytochrome c / hydrogenase / hmc operon | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Desulfovibrio desulfuricans (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.89 Å | |||||||||
Authors | Umhau, S. / Fritz, G. / Diederichs, K. / Breed, J. / Kroneck, P.M. / Welte, W. | |||||||||
Citation | Journal: Biochemistry / Year: 2001 Title: Three-dimensional structure of the nonaheme cytochrome c from Desulfovibrio desulfuricans Essex in the Fe(III) state at 1.89 A resolution. Authors: Umhau, S. / Fritz, G. / Diederichs, K. / Breed, J. / Welte, W. / Kroneck, P.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1duw.cif.gz | 87.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1duw.ent.gz | 71.5 KB | Display | PDB format |
PDBx/mmJSON format | 1duw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1duw_validation.pdf.gz | 3.4 MB | Display | wwPDB validaton report |
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Full document | 1duw_full_validation.pdf.gz | 3.4 MB | Display | |
Data in XML | 1duw_validation.xml.gz | 20.1 KB | Display | |
Data in CIF | 1duw_validation.cif.gz | 30.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/du/1duw ftp://data.pdbj.org/pub/pdb/validation_reports/du/1duw | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 31727.299 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: DESUFOVIBRIO DESULFURICANS STRAIN: ESSEX6 COLLECTION: ATCC 29577 Source: (natural) Desulfovibrio desulfuricans (bacteria) / Strain: ESSEX6 / References: UniProt: Q9XCU0 | ||||
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#2: Chemical | ChemComp-HEC / #3: Chemical | ChemComp-GOL / | #4: 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: 2.86 Å3/Da / Density % sol: 57.01 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG 4000, Isopropanol, HEPES pH 7.5, , VAPOR DIFFUSION, HANGING DROP, temperature 18K | ||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 49 % | ||||||||||||||||||||||||
Crystal grow | *PLUS Details: drop consists of equal amounts of protein and precipitant solutions | ||||||||||||||||||||||||
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: 0.83 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.83 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→50 Å / Num. all: 101894 / Num. obs: 27269 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.079 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.89→1.98 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.187 / Num. unique all: 3249 / % possible all: 80.6 |
Reflection | *PLUS Highest resolution: 1.89 Å / Lowest resolution: 30 Å / Num. measured all: 101894 |
Reflection shell | *PLUS % possible obs: 80.6 % / Mean I/σ(I) obs: 3.4 |
-Processing
Software |
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Refinement | Resolution: 1.89→30 Å / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 1.89→30 Å
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Refine LS restraints |
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Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.204 / Rfactor Rwork: 0.182 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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