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- PDB-5xie: Crystal Structure of HasAp with 5-ethynyl-10,20-diphenylporphyrin -
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Open data
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Basic information
Entry | Database: PDB / ID: 5xie | ||||||
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Title | Crystal Structure of HasAp with 5-ethynyl-10,20-diphenylporphyrin | ||||||
![]() | Heme acquisition protein HasAp | ||||||
![]() | TRANSPORT PROTEIN / HEME ACQUISITION PROTEIN | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Shoji, O. / Uehara, H. / Sugimoto, H. / Shiro, Y. / Watanabe, Y. | ||||||
![]() | ![]() Title: Structures of the Heme Acquisition Protein HasA with Iron(III)-5,15-Diphenylporphyrin and Derivatives Thereof as an Artificial Prosthetic Group Authors: Uehara, H. / Shisaka, Y. / Nishimura, T. / Sugimoto, H. / Shiro, Y. / Miyake, Y. / Shinokubo, H. / Watanabe, Y. / Shoji, O. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 86.7 KB | Display | ![]() |
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PDB format | ![]() | 65.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xa4C ![]() 5xibC ![]() 5xicC ![]() 5xkbC ![]() 3w8oS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 18901.535 Da / Num. of mol.: 2 / Fragment: UNP Residues 1-184 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: PAO1 / Gene: hasAp, PA3407 / Plasmid: PQE30 / Production host: ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.32 Å3/Da / Density % sol: 62.93 % / Mosaicity: 0.622 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 50mM HEPES (pH7.5), 50mM KPi buffer (pH7.0), 0.63M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 28, 2015 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 2.05→50 Å / Num. obs: 31662 / % possible obs: 99.8 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.019 / Rrim(I) all: 0.06 / Χ2: 1.018 / Net I/σ(I): 20 / Num. measured all: 329462 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3W8O Resolution: 2.05→18.8 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.1896 / FOM work R set: 0.8913 / SU B: 3.017 / SU ML: 0.083 / SU R Cruickshank DPI: 0.1469 / SU Rfree: 0.1339 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.147 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.59 Å2 / Biso mean: 25.532 Å2 / Biso min: 13.79 Å2
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Refinement step | Cycle: final / Resolution: 2.05→18.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.053→2.105 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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