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Yorodumi- PDB-6jlg: Crystal Structure of HasAp with Co-9,10,19,20-Tetraphenylporphycene -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jlg | ||||||
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Title | Crystal Structure of HasAp with Co-9,10,19,20-Tetraphenylporphycene | ||||||
Components | Heme acquisition protein HasA | ||||||
Keywords | TRANSPORT PROTEIN / HEME ACQUISITION PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Pseudomonas aeruginosa (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Sakakibara, E. / Shisaka, Y. / Onoda, H. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O. | ||||||
Funding support | Japan, 1items
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Citation | Journal: Rsc Adv / Year: 2019 Title: Highly malleable haem-binding site of the haemoprotein HasA permits stable accommodation of bulky tetraphenylporphycenes. Authors: Sakakibara, E. / Shisaka, Y. / Onoda, H. / Koga, D. / Xu, N. / Ono, T. / Hisaeda, Y. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. / Shoji, O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jlg.cif.gz | 546.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jlg.ent.gz | 454.1 KB | Display | PDB format |
PDBx/mmJSON format | 6jlg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6jlg_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 6jlg_full_validation.pdf.gz | 2.9 MB | Display | |
Data in XML | 6jlg_validation.xml.gz | 59 KB | Display | |
Data in CIF | 6jlg_validation.cif.gz | 76.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jl/6jlg ftp://data.pdbj.org/pub/pdb/validation_reports/jl/6jlg | HTTPS FTP |
-Related structure data
Related structure data | 3ellS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
-Components
#1: Protein | Mass: 18901.535 Da / Num. of mol.: 8 / Fragment: Residues 1-184 / Mutation: Wild-type Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) Gene: hasA, C0044_25535, C8257_08650, CAZ10_20450, CGU42_19580, DT376_18720, DZ940_32815, NCTC13719_01562, PAERUG_E15_London_28_01_14_06674, PAMH19_1664, RW109_RW109_02394 Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: A0A069Q9Z5, UniProt: G3XD33*PLUS #2: Chemical | ChemComp-BWU / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.31 Å3/Da / Density % sol: 62.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM HEPES/HCl (pH7.5), 1260mM Ammonium sulfate / PH range: 7.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jun 6, 2018 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→46.83 Å / Num. obs: 68363 / % possible obs: 99.7 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.249 / Net I/σ(I): 7 |
Reflection shell | Resolution: 2.5→2.56 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.898 / Num. unique obs: 4603 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELL Resolution: 2.5→45.79 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 21.623 / SU ML: 0.219 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.403 / ESU R Free: 0.254 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→45.79 Å
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Refine LS restraints |
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