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- PDB-7emv: Crystal Structure of the HasAp V37G Mutant Capturing Iron-5,10,15... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7emv | ||||||||||||
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Title | Crystal Structure of the HasAp V37G Mutant Capturing Iron-5,10,15-Triphenylporphyrin | ||||||||||||
![]() | 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 / IMIDAZOLE / 5,10,15-Triphenylporphyrin cpntaining FE / 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 | ![]() | 96.1 KB | Display | ![]() |
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PDB format | ![]() | 70.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 783.4 KB | Display | ![]() |
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Full document | ![]() | 785.3 KB | Display | |
Data in XML | ![]() | 10.4 KB | Display | |
Data in CIF | ![]() | 14.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7emoC ![]() 7empC ![]() 7emqC ![]() 7emrC ![]() 7emsC ![]() 7emtC ![]() 7emuC ![]() 7emwC ![]() 7vm1C ![]() 5xicS 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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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 18788.377 Da / Num. of mol.: 1 / Mutation: V37G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: ![]() ![]() |
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#2: Chemical | ChemComp-WXP / |
#3: Chemical | ChemComp-IMD / |
#4: Chemical | ChemComp-GOL / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.18 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100mM Imidazole/HCl (pH 8.0), 30% PEG 8000, 0.2M NaCl |
-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: 1.45→45.74 Å / Num. obs: 29690 / % possible obs: 99.6 % / Redundancy: 25.9 % / CC1/2: 1 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.017 / Rrim(I) all: 0.089 / Net I/σ(I): 25 / Num. measured all: 768780 / Scaling rejects: 36 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5XIC Resolution: 1.45→20 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.521 / SU ML: 0.042 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.063 / 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: 54.44 Å2 / Biso mean: 18.55 Å2 / Biso min: 11.19 Å2
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Refinement step | Cycle: final / Resolution: 1.45→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.45→1.487 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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