+
Open data
-
Basic information
Entry | Database: PDB / ID: 2vz7 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Crystal structure of the YC-17-bound PikC D50N mutant | |||||||||
![]() | CYTOCHROME P450 MONOOXYGENASE | |||||||||
![]() | OXIDOREDUCTASE / ANTIBIOTIC BIOSYNTHESIS / PIKC / IRON / HEME / CYP107L1 / MONOOXYGENASE / MACROLIDE MONOOXYGENASE / METAL-BINDING / CYTOCHROME P450 | |||||||||
Function / homology | ![]() pikromycin synthase / macrolide biosynthetic process / cholest-4-en-3-one 26-monooxygenase activity / steroid hydroxylase activity / cholesterol catabolic process / monooxygenase activity / iron ion binding / heme binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Li, S. / Sherman, D.H. / Podust, L.M. | |||||||||
![]() | ![]() Title: Analysis of Transient and Catalytic Desosamine Binding Pockets in Cytochrome P450 Pikc from Streptomyces Venezuelae. Authors: Li, S. / Ouellet, H. / Sherman, D.H. / Podust, L.M. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 171.2 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 134.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 1.6 MB | Display | |
Data in XML | ![]() | 38 KB | Display | |
Data in CIF | ![]() | 50.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2vzmC ![]() 2c6hS S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.99995, -0.00983, 0.00135), Vector: |
-
Components
#1: Protein | Mass: 48267.758 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Compound details | ENGINEERED | Sequence details | ENGINEERED | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.66 Å3/Da / Density % sol: 53 % / Description: NONE |
---|---|
Crystal grow | Temperature: 296 K / pH: 6.5 Details: 20% PEG 4000; 0.1 M BIS-TRIS, PH 6.5; 0.2 M LITHIUM SULFATE; T=23 C |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 26, 2007 / Details: MIRRORS |
Radiation | Monochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.11587 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. obs: 17318 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.7 / % possible all: 99.9 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2C6H Resolution: 3.2→49.67 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 46156.97 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: BULK SOLVENT MODEL USED, DISORDERED REGIONS WERE OMITTED FROM THE STRUCTURE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 34.4423 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.2→49.67 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.2→3.4 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
|