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Open data
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Basic information
Entry | Database: PDB / ID: 1i54 | |||||||||
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Title | CYTOCHROME C (TUNA) 2FE:1ZN MIXED-METAL PORPHYRINS | |||||||||
![]() | CYTOCHROME C | |||||||||
![]() | ELECTRON TRANSPORT / cytochrome c / zinc-porphyrin / mixed-metal | |||||||||
Function / homology | ![]() mitochondrial electron transport, cytochrome c to oxygen / mitochondrial electron transport, ubiquinol to cytochrome c / respirasome / mitochondrial intermembrane space / electron transfer activity / heme binding / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Crane, B.R. / Tezcan, F.A. / Winkler, J.R. / Gray, H.B. | |||||||||
![]() | ![]() Title: Electron tunneling in protein crystals. Authors: Tezcan, F.A. / Crane, B.R. / Winkler, J.R. / Gray, H.B. | |||||||||
History |
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Remark 600 | HETEROGEN The residue 1104 of HEM and residue 1105 of ZNH are alternate conformers with occupancy ...HETEROGEN The residue 1104 of HEM and residue 1105 of ZNH are alternate conformers with occupancy of 0.68 and 0.32, respectively. In similar residue 1106 of HEM and residue 1107 of ZNH are alternate conformers with occupancy 0.68 and 0.32, respectively. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 67.5 KB | Display | ![]() |
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PDB format | ![]() | 48 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 694 KB | Display | ![]() |
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Full document | ![]() | 703.5 KB | Display | |
Data in XML | ![]() | 7.3 KB | Display | |
Data in CIF | ![]() | 12.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1i55C ![]() 3cytS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 11390.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.67 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 Details: (NH4)2SO4 NaCL NaPi, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 28, 2000 / Details: mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→30 Å / Num. all: 27877 / Num. obs: 27877 / % possible obs: 97.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.2 % / Biso Wilson estimate: 16.7 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.232 / % possible all: 68.4 |
Reflection | *PLUS |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 3CYT Resolution: 1.5→21.1 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 529342.82 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: Crystals contain a 2:1 mixture of Fe- and Zn-porphyrin. Residues 1104 and 1105 and residues 1106 and 1107 were refined as non-interacting metalloporphyrins of occupancies determined from ...Details: Crystals contain a 2:1 mixture of Fe- and Zn-porphyrin. Residues 1104 and 1105 and residues 1106 and 1107 were refined as non-interacting metalloporphyrins of occupancies determined from anomalous scattering experiments. No stereochemical restraints on Fe and Zn interactions
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 23.62 Å2 / ksol: 0.383 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→21.1 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.55 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 10
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Xplor file |
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Software | *PLUS Name: CNS / Version: 1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 8 % | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 14.1 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.396 / % reflection Rfree: 7.6 % / Rfactor Rwork: 0.385 |