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Yorodumi- PDB-4jet: 2.2A resolution structure of Holo hemophore HasA from Yersinia pestis -
+Open data
-Basic information
Entry | Database: PDB / ID: 4jet | ||||||
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Title | 2.2A resolution structure of Holo hemophore HasA from Yersinia pestis | ||||||
Components | Hemophore HasA | ||||||
Keywords | HEME BINDING PROTEIN / TRANSPORT PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Yersinia pestis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | ||||||
Authors | Kumar, R. / Lovell, S. / Battaile, K.P. / Rivera, M. | ||||||
Citation | Journal: Biochemistry / Year: 2013 Title: The Hemophore HasA from Yersinia pestis (HasAyp) Coordinates Hemin with a Single Residue, Tyr75, and with Minimal Conformational Change. Authors: Kumar, R. / Lovell, S. / Matsumura, H. / Battaile, K.P. / Moenne-Loccoz, P. / Rivera, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jet.cif.gz | 369.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jet.ent.gz | 304.1 KB | Display | PDB format |
PDBx/mmJSON format | 4jet.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/je/4jet ftp://data.pdbj.org/pub/pdb/validation_reports/je/4jet | HTTPS FTP |
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-Related structure data
Related structure data | 4jerSC 4jesC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 21025.088 Da / Num. of mol.: 10 / Fragment: UNP residues 1-193 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Yersinia pestis (bacteria) / Gene: hasA, y0314, YP_3127, YPO3922 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-GOLD (DE3) / References: UniProt: Q7CL15, UniProt: Q0WA92*PLUS #2: Chemical | ChemComp-HEM / #3: Chemical | ChemComp-CL / #4: 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: 2.64 Å3/Da / Density % sol: 53.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.8 Details: 20% (w/v) PEG 3350, 50 mM Ches, 200 mM magnesium formate dihydrate, pH 8.8, vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→228.701 Å / Num. all: 109337 / Num. obs: 109337 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2 / Num. unique all: 5397 / % possible all: 97.7 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 4JER Resolution: 2.2→38.624 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.29 / σ(F): 1.84 / Phase error: 22.55 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.8 Å2 / Biso mean: 31.7917 Å2 / Biso min: 10.39 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→38.624 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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