+Open data
-Basic information
Entry | Database: PDB / ID: 6u87 | ||||||
---|---|---|---|---|---|---|---|
Title | Pseudomonas aeruginosa HasA mutant - Y75H | ||||||
Components | HasAp | ||||||
Keywords | METAL BINDING PROTEIN / HasA / hemophore | ||||||
Function / homology | Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / PROTOPORPHYRIN IX CONTAINING FE / HasAp Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Brimberry, M. / Lanzilotta, W. / Wilks, A. / Dent, A. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Biochemistry / Year: 2021 Title: Axial Heme Coordination by the Tyr-His Motif in the Extracellular Hemophore HasAp Is Critical for the Release of Heme to the HasR Receptor of Pseudomonas aeruginosa . Authors: Dent, A.T. / Brimberry, M. / Albert, T. / Lanzilotta, W.N. / Moenne-Loccoz, P. / Wilks, A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6u87.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6u87.ent.gz | 37.4 KB | Display | PDB format |
PDBx/mmJSON format | 6u87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6u87_validation.pdf.gz | 787.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 6u87_full_validation.pdf.gz | 788.2 KB | Display | |
Data in XML | 6u87_validation.xml.gz | 10.9 KB | Display | |
Data in CIF | 6u87_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u8/6u87 ftp://data.pdbj.org/pub/pdb/validation_reports/u8/6u87 | HTTPS FTP |
-Related structure data
Related structure data | 3ellS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 20889.789 Da / Num. of mol.: 1 / Mutation: Y75H Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: hasAp, IPC3_06435 / Production host: Escherichia coli (E. coli) / References: UniProt: O69756 |
---|---|
#2: Chemical | ChemComp-HEM / |
#3: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.72 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop Details: 0.1M NaCl, 0.1M HEPES pH 7.5, 1.6M Ammonium Sulfate |
-Data collection
Diffraction | Mean temperature: 291 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 25, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.3→34.456 Å / Num. obs: 40083 / % possible obs: 96.4 % / Redundancy: 14.7 % / CC1/2: 0.957 / Net I/σ(I): 6.9 |
Reflection shell | Resolution: 1.32→1.39 Å / Num. unique obs: 116 / CC1/2: 0.957 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELL Resolution: 1.3→34.456 Å / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 16.38
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 57.9 Å2 / Biso mean: 15.2499 Å2 / Biso min: 7.31 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.3→34.456 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|