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Yorodumi- PDB-4xzd: Crystal Structure of Wild-type HasA from Yersinia pseudotuberculosis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4xzd | |||||||||
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Title | Crystal Structure of Wild-type HasA from Yersinia pseudotuberculosis | |||||||||
Components | Extracellular heme acquisition hemophore HasA | |||||||||
Keywords | HEME BINDING PROTEIN / heme acquisition system / hemophore | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Yersinia pseudotuberculosis IP 32953 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.7 Å | |||||||||
Authors | Kanadani, M. / Hino, T. / Nagano, S. / Sato, T. / Ozaki, S. | |||||||||
Funding support | Japan, 2items
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Citation | Journal: J.Inorg.Biochem. / Year: 2015 Title: The crystal structure of heme acquisition system A from Yersinia pseudotuberculosis (HasAypt): Roles of the axial ligand Tyr75 and two distal arginines in heme binding Authors: Kanadani, M. / Sato, T. / Hino, T. / Nagano, S. / Ozaki, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4xzd.cif.gz | 101.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4xzd.ent.gz | 74.3 KB | Display | PDB format |
PDBx/mmJSON format | 4xzd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xz/4xzd ftp://data.pdbj.org/pub/pdb/validation_reports/xz/4xzd | HTTPS FTP |
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-Related structure data
Related structure data | 4y1qC 4y4sC 1dk0S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 23649.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pseudotuberculosis IP 32953 (bacteria) Strain: IP32953 / Gene: HasA, YPTB0114 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: Q66G68 #2: Chemical | #3: 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: 2.23 Å3/Da / Density % sol: 44.88 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris HCl, 1.1 M Na-citrate, 1.5% 1,6-hexandiol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.93 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Jul 10, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.7→81.338 Å / Num. all: 45941 / Num. obs: 45941 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 13.88 Å2 / Rpim(I) all: 0.068 / Rrim(I) all: 0.129 / Rsym value: 0.109 / Net I/av σ(I): 4.929 / Net I/σ(I): 8.1 / Num. measured all: 162443 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1DK0 Resolution: 1.7→35.656 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→35.656 Å
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Refine LS restraints |
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LS refinement shell |
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