+Open data
-Basic information
Entry | Database: PDB / ID: 2j1m | ||||||
---|---|---|---|---|---|---|---|
Title | P450 BM3 Heme domain in complex with DMSO | ||||||
Components | CYTOCHROME P450 102 | ||||||
Keywords | OXIDOREDUCTASE / DMSO-INHIBITION / P450 / IRON / HEME / ORGANIC SOLVENT / FLAVOPROTEIN / MONOOXYGENASE / METAL-BINDING / MEMBRANE | ||||||
Function / homology | Function and homology information NADPH-hemoprotein reductase / NADPH-hemoprotein reductase activity / oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen / unspecific monooxygenase / aromatase activity / metabolic process / FMN binding / iron ion binding / heme binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | BACILLUS MEGATERIUM (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Kuper, J. / Tuck-Seng, W. / Roccatano, D. / Wilmanns, M. / Schwaneberg, U. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2007 Title: Understanding a Mechanism of Organic Cosolvent Inactivation in Heme Monooxygenase P450 Bm-3. Authors: Kuper, J. / Wong, T.S. / Roccatano, D. / Wilmanns, M. / Schwaneberg, U. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2j1m.cif.gz | 220.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2j1m.ent.gz | 176.4 KB | Display | PDB format |
PDBx/mmJSON format | 2j1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/2j1m ftp://data.pdbj.org/pub/pdb/validation_reports/j1/2j1m | HTTPS FTP |
---|
-Related structure data
Related structure data | 2j4sC 1bu7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.6072, 0.7938, -0.03358), Vector: |
-Components
#1: Protein | Mass: 52169.461 Da / Num. of mol.: 2 / Fragment: HEME DOMAIN, RESIDUES 1-455 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BACILLUS MEGATERIUM (bacteria) / Plasmid: PETM11 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P14779, unspecific monooxygenase #2: Chemical | #3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-DMS / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54.7 % |
---|---|
Crystal grow | Details: 0.04 M ZINC ACETATE, 15 % (W/V) PEG3350, 14 % (V/V) DMSO |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.98 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→38.35 Å / Num. obs: 125177 / % possible obs: 100 % / Redundancy: 6.64 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 15.33 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 6.54 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 2.3 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BU7 Resolution: 1.7→36.04 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.51 / SU ML: 0.062 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.092 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.45 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→36.04 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|