[English] 日本語
Yorodumi- PDB-4hip: Crystal structure of the Pseudomonas aeruginosa azurin, H126NO YOH109 -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hip | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the Pseudomonas aeruginosa azurin, H126NO YOH109 | ||||||
Components | Azurin | ||||||
Keywords | ELECTRON TRANSPORT / Greek key / Electron Transfer / Nitrosylated | ||||||
Function / homology | Function and homology information transition metal ion binding / periplasmic space / electron transfer activity / copper ion binding / zinc ion binding / identical protein binding Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Herrera, N. / Warren, J.J. / Gray, H.B. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Electron Flow through Nitrotyrosinate in Pseudomonas aeruginosa Azurin. Authors: Warren, J.J. / Herrera, N. / Hill, M.G. / Winkler, J.R. / Gray, H.B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4hip.cif.gz | 57.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4hip.ent.gz | 46.2 KB | Display | PDB format |
PDBx/mmJSON format | 4hip.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hi/4hip ftp://data.pdbj.org/pub/pdb/validation_reports/hi/4hip | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
3 |
| ||||||||
4 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 13996.777 Da / Num. of mol.: 2 / Mutation: W68F,Y92F,H103Q,Y128F,K142NIY,T146H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: azu, PA4922 / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: P00282 #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.13 Å3/Da / Density % sol: 42.14 % |
---|---|
Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: 26-34% PEG 4000, 100 mM Lithium Nitrate, 6.25 mM Copper Sulfate and 100 mM Imidazole, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 19, 2012 / Details: K-B focusing mirrors |
Radiation | Monochromator: Liquid nitrogen-cooled double crystal, Si 111 Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.7997→36.5025 Å / Num. all: 21310 / % possible obs: 97.2 % / Observed criterion σ(I): 59.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→36.5 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.895 / SU B: 5.471 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.213 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.115 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.9→36.5 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
|