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Open data
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Basic information
Entry | Database: PDB / ID: 7emr | ||||||||||||
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Title | Crystal Structure of HasAp Capturing Cobalt Tetraphenylporphyrin | ||||||||||||
![]() | Heme acquisition protein HasAp | ||||||||||||
![]() | TRANSPORT PROTEIN / HEME ACQUISITION PROTEIN | ||||||||||||
Function / homology | Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Co-5,10,15,20-Tetraphenylporphyrin / PHOSPHATE ION / Heme acquisition protein HasAp![]() | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Shisaka, Y. / Sakakibara, E. / Sugimoto, H. / Shoji, O. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Tetraphenylporphyrin Enters the Ring: First Example of a Complex between Highly Bulky Porphyrins and a Protein. Authors: Shisaka, Y. / Sakakibara, E. / Suzuki, K. / Stanfield, J.K. / Onoda, H. / Ueda, G. / Hatano, M. / Sugimoto, H. / 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 | ![]() | 240 KB | Display | ![]() |
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PDB format | ![]() | 191.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 25.7 KB | Display | |
Data in CIF | ![]() | 35.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7emoC ![]() 7empC ![]() 7emqC ![]() 7emsC ![]() 7emtC ![]() 7emuC ![]() 7emvC ![]() 7emwC ![]() 7vm1C ![]() 3ellS S: Starting model for refinement C: citing same article ( |
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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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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 3 molecules ABC
#1: Protein | Mass: 18901.535 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 275 molecules ![](data/chem/img/J83.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NHE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/CXS.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NHE / | #4: Chemical | #5: Chemical | ChemComp-PO4 / #6: Chemical | #7: 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: 2.68 Å3/Da / Density % sol: 54.14 % / Mosaicity: 0.16 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 10.5 Details: 100mM CAPS/NaOH (pH 10.5), 1.2M Sodium phosphate monobasic/0.8M pottasium phosphate dibasic, 0.2M lithium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX225-HS / Detector: CCD / Date: Dec 18, 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: 1.55→48.92 Å / Num. obs: 86763 / % possible obs: 100 % / Redundancy: 14.9 % / CC1/2: 1 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.019 / Rrim(I) all: 0.073 / Net I/σ(I): 22 / Num. measured all: 1295135 / Scaling rejects: 13 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3ELL Resolution: 1.55→20 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 2.695 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.061 / 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: 83.97 Å2 / Biso mean: 24.251 Å2 / Biso min: 15.19 Å2
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Refinement step | Cycle: final / Resolution: 1.55→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.59 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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