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- PDB-1k2o: Cytochrome P450Cam with Bound BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1k2o | ||||||
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Title | Cytochrome P450Cam with Bound BIS(2,2'-BIPYRIDINE)-(5-METHYL-2-2'-BIPYRIDINE)-C2-ADAMANTANE RUTHENIUM (II) | ||||||
![]() | Cytochrome P450CAM | ||||||
![]() | OXIDOREDUCTASE / P450 / monooxygenase / electron transfer / energy transfer / fluorinated aromatics / biphenyl / adamantane / ruthenium channel / substrate-binding | ||||||
Function / homology | ![]() camphor 5-monooxygenase / camphor 5-monooxygenase activity / (+)-camphor catabolic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / iron ion binding / heme binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Dunn, A.R. / Dmochowski, I.J. / Bilwes, A.M. / Gray, H.B. / Crane, B.R. | ||||||
![]() | ![]() Title: Probing the open state of cytochrome P450cam with ruthenium-linker substrates. Authors: Dunn, A.R. / Dmochowski, I.J. / Bilwes, A.M. / Gray, H.B. / Crane, B.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 202.2 KB | Display | ![]() |
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PDB format | ![]() | 158 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2cppS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 46556.816 Da / Num. of mol.: 2 / Mutation: C334A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 705 molecules ![](data/chem/img/CAC.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RFA.gif)
![](data/chem/img/RFB.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HEM.gif)
![](data/chem/img/RFA.gif)
![](data/chem/img/RFB.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CAC / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: slow cooling / pH: 7.5 Details: Hepes, PEG, KCL, DTT, pH 7.5, slow cooling, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / 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: MARRESEARCH / Detector: IMAGE PLATE / Date: May 24, 2000 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.72 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→28 Å / Num. all: 111741 / Num. obs: 111741 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 19 Å2 / Rsym value: 0.038 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.65→1.71 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.292 / % possible all: 97 |
Reflection | *PLUS Rmerge(I) obs: 0.038 |
Reflection shell | *PLUS % possible obs: 97 % / Rmerge(I) obs: 0.292 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2cpp Resolution: 1.65→19.81 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 819940.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.6776 Å2 / ksol: 0.349301 e/Å3 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.71 Å / Rfactor Rfree error: 0.01 / 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 % / Rfactor obs: 0.21 / Rfactor Rwork: 0.21 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.6 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.287 / % reflection Rfree: 8.5 % / Rfactor Rwork: 0.292 |