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- PDB-7vf8: Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation -
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Open data
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Basic information
Entry | Database: PDB / ID: 7vf8 | ||||||||||||||||||||||||
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Title | Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation | ||||||||||||||||||||||||
![]() | Heme acquisition protein HasAp | ||||||||||||||||||||||||
![]() | METAL TRANSPORT / Heme acquisition protein | ||||||||||||||||||||||||
Function / homology | Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Co-5-octaethyloxaporphyrinium cation / CITRIC ACID / DI(HYDROXYETHYL)ETHER / Heme acquisition protein HasAp![]() | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||||||||||||||
![]() | Takiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal Structure of HasAp with Co-5-octaethyloxaporphyrinium cation Authors: Takiguchi, A. / Sakakibara, E. / Sugimoto, H. / Shoji, O. / Shinokubo, H. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 188.5 KB | Display | ![]() |
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PDB format | ![]() | 151.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 30.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5xa4S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#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.) ![]() Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 346 molecules ![](data/chem/img/7KI.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CIT / | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.41 Å3/Da / Density % sol: 63.94 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 1.0M potassium sodium tartrate, 100mM imidazole/hydrochloric acid (pH 8.0), 200mM sodium chloride |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2021 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.35→44.45 Å / Num. obs: 111120 / % possible obs: 98.5 % / Redundancy: 20.056 % / Biso Wilson estimate: 23.368 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.122 / Rrim(I) all: 0.125 / Χ2: 0.779 / Net I/σ(I): 21.25 / Num. measured all: 2228601 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XA4 Resolution: 1.35→44.45 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.323 / SU ML: 0.023 / SU R Cruickshank DPI: 0.0396 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.037 / 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: 80.63 Å2 / Biso mean: 18.002 Å2 / Biso min: 6.29 Å2
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Refinement step | Cycle: final / Resolution: 1.35→44.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.384 Å / Rfactor Rfree error: 0
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