[English] 日本語
Yorodumi- PDB-1pf3: Crystal Structure of the M441L mutant of the multicopper oxidase CueO -
+Open data
-Basic information
Entry | Database: PDB / ID: 1pf3 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal Structure of the M441L mutant of the multicopper oxidase CueO | ||||||
Components | Blue copper oxidase cueO | ||||||
Keywords | OXIDOREDUCTASE / copper / multicopper oxidase | ||||||
Function / homology | Function and homology information cuproxidase / oxidoreductase activity, acting on metal ions, oxygen as acceptor / oxidoreductase activity, acting on metal ions / detoxification of copper ion / oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor / response to copper ion / ferroxidase activity / outer membrane-bounded periplasmic space / periplasmic space / copper ion binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å | ||||||
Authors | Roberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: A Labile Regulatory Copper Ion Lies Near the T1 Copper Site in the Multicopper Oxidase CueO. Authors: Roberts, S.A. / Wildner, G.F. / Grass, G. / Weichsel, A. / Ambrus, A. / Rensing, C. / Montfort, W.R. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1pf3.cif.gz | 114.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1pf3.ent.gz | 85.2 KB | Display | PDB format |
PDBx/mmJSON format | 1pf3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pf/1pf3 ftp://data.pdbj.org/pub/pdb/validation_reports/pf/1pf3 | HTTPS FTP |
---|
-Related structure data
Related structure data | 1n68C 1kv7S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 54651.520 Da / Num. of mol.: 1 / Mutation: M441L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: CUEO / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P36649 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | ChemComp-C2C / | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.46 % |
---|---|
Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 20% PEG, 200 mM ammonium acetate, 100 mM sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 22K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 5, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→10 Å / Num. all: 63714 / Num. obs: 63714 / % possible obs: 86 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rsym value: 0.066 / Net I/σ(I): 20.2 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 2.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 7119 / Rsym value: 0.18 / % possible all: 94 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: pdb entry 1KV7 Resolution: 1.5→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 1.227 / SU ML: 0.048 Isotropic thermal model: Isotropic, except copper, chlorine anisotropic Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1- ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The T1 copper is partially depleted (around 50% occupancy) The T2 copper is somewhat less depleted. MISSING FROM THE MODEL ARE RESIDUES 1-30 AT THE N-TERMINUS (1-28 ARE A PRESUMABLY CLEAVED SIGNAL PEPTIDE, 29-30 ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP), AND RESIDUES 380-402 WHICH ARE NOT VISIBLE IN THE ELECTRON DENSITY MAP AND, PRESUMABLY, DISORDERED. A strep tag on the C terminus has not been cleaved but is not visible in the electron density maps.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15.712 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20 /
|