[English] 日本語
Yorodumi- PDB-4o6s: 1.32A resolution structure of the hemophore HasA from Pseudomonas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4o6s | ||||||
---|---|---|---|---|---|---|---|
Title | 1.32A resolution structure of the hemophore HasA from Pseudomonas aeruginosa (H83A mutant, Zinc Bound) | ||||||
Components | HasAp | ||||||
Keywords | Heme Binding Protein / Hemophore / Y75 Loop | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.32 Å | ||||||
Authors | Lovell, S. / Kumar, R. / Battaile, K.P. / Matsumura, H. / Yao, H. / Rodriguez, J.C. / Moenne-Loccoz, P. / Rivera, M. | ||||||
Citation | Journal: Biochemistry / Year: 2014 Title: Replacing the Axial Ligand Tyrosine 75 or Its Hydrogen Bond Partner Histidine 83 Minimally Affects Hemin Acquisition by the Hemophore HasAp from Pseudomonas aeruginosa. Authors: Kumar, R. / Matsumura, H. / Lovell, S. / Yao, H. / Rodriguez, J.C. / Battaile, K.P. / Moenne-Loccoz, P. / Rivera, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4o6s.cif.gz | 96.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4o6s.ent.gz | 71.2 KB | Display | PDB format |
PDBx/mmJSON format | 4o6s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4o6s_validation.pdf.gz | 825.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4o6s_full_validation.pdf.gz | 827.1 KB | Display | |
Data in XML | 4o6s_validation.xml.gz | 12.2 KB | Display | |
Data in CIF | 4o6s_validation.cif.gz | 17.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o6/4o6s ftp://data.pdbj.org/pub/pdb/validation_reports/o6/4o6s | HTTPS FTP |
-Related structure data
Related structure data | 4o6qC 4o6tC 4o6uC 3ellS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 18834.465 Da / Num. of mol.: 1 / Mutation: H83A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hasAp / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: O69756 | ||||||
---|---|---|---|---|---|---|---|
#2: Chemical | ChemComp-EDO / #3: Chemical | ChemComp-HEM / | #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.73 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 10% (v/V) isopropanol, 100mM Na Cacodylate, 200mM Zinc Acetate, pH 6.5, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2010 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.32→40.682 Å / Num. all: 43290 / Num. obs: 43290 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 10.2 Å2 / Rsym value: 0.095 / Net I/σ(I): 7.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Phasing
Phasing | Method: molecular replacement | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phasing MR |
|
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELL Resolution: 1.32→34.628 Å / Occupancy max: 1 / Occupancy min: 0.33 / SU ML: 0.16 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 14.79 / Stereochemistry target values: ML
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 1.01 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 29.939 Å2 / ksol: 0.413 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 42.67 Å2 / Biso mean: 12.9965 Å2 / Biso min: 4.01 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.32→34.628 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
|