+Open data
-Basic information
Entry | Database: PDB / ID: 1ft6 | |||||||||
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Title | REDUCED STATE OF CYTOCHROME C554 FROM NITROSOMONAS EUROPAEA | |||||||||
Components | CYTOCHROME C554 | |||||||||
Keywords | ELECTRON TRANSPORT / heme-stacking | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Nitrosomonas europaea (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.8 Å | |||||||||
Authors | Iverson, T.M. / Arciero, D.M. / Hooper, A.B. / Rees, D.C. | |||||||||
Citation | Journal: J.Biol.Inorg.Chem. / Year: 2001 Title: High-resolution structures of the oxidized and reduced states of cytochrome c554 from Nitrosomonas europaea. Authors: Iverson, T.M. / Arciero, D.M. / Hooper, A.B. / Rees, D.C. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: Heme Packing Motifs Revealed by the Crystal Structure of the Tetra-heme Cytochrome c554 from Nitrosomonas europaea Authors: Iverson, T.M. / Arciero, D.M. / Hsu, B.T. / Logan, M.S. / Hooper, A.B. / Rees, D.C. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ft6.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ft6.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ft6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ft6_validation.pdf.gz | 756.3 KB | Display | wwPDB validaton report |
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Full document | 1ft6_full_validation.pdf.gz | 761.2 KB | Display | |
Data in XML | 1ft6_validation.xml.gz | 7 KB | Display | |
Data in CIF | 1ft6_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/1ft6 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/1ft6 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 23656.900 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Nitrosomonas europaea (bacteria) / References: UniProt: Q57142 |
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-Non-polymers , 5 types, 149 molecules
#2: Chemical | ChemComp-SO3 / | ||||
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#3: Chemical | ChemComp-PO4 / | ||||
#4: Chemical | ChemComp-HEC / #5: Chemical | ChemComp-DTN / | #6: 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: 2.99 Å3/Da / Density % sol: 58.81 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 10.1 Details: 62.5% w/vol potassium phosphate pH 10.1, VAPOR DIFFUSION, SITTING DROP, temperature 295K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 72 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, sitting drop / Details: Iverson, T.M., (1998) Nat.Struct.Biol., 5, 1005. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1.08 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 23, 1998 |
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→20 Å / Num. all: 112676 / Num. obs: 24588 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 31.3 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 28.5 |
Reflection shell | Resolution: 1.8→1.88 Å / Rmerge(I) obs: 0.288 / % possible all: 85.9 |
Reflection | *PLUS Num. measured all: 112676 |
Reflection shell | *PLUS % possible obs: 85.9 % / Mean I/σ(I) obs: 5.1 |
-Processing
Software |
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Refinement | Resolution: 1.8→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh and Huber
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Refinement step | Cycle: LAST / Resolution: 1.8→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.8 Å / Lowest resolution: 20 Å / σ(F): 0 / Rfactor obs: 0.197 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS
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