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Yorodumi- PDB-7emu: Crystal Structure of the HasAp V37G Mutant Capturing Manganese Te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7emu | ||||||||||||
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Title | Crystal Structure of the HasAp V37G Mutant Capturing Manganese Tetraphenylporphyrin | ||||||||||||
Components | Heme acquisition protein HasAp | ||||||||||||
Keywords | TRANSPORT PROTEIN / HEME ACQUISITION PROTEIN | ||||||||||||
Function / homology | Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / metal ion binding / Mn-5,10,15,20-Tetraphenylporphyrin / Heme acquisition protein HasAp Function and homology information | ||||||||||||
Biological species | Pseudomonas aeruginosa str. PAO1 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å | ||||||||||||
Authors | Shisaka, Y. / Sakakibara, E. / Sugimoto, H. / Shoji, O. | ||||||||||||
Funding support | Japan, 3items
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Citation | Journal: Chembiochem / Year: 2022 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7emu.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7emu.ent.gz | 73.5 KB | Display | PDB format |
PDBx/mmJSON format | 7emu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7emu_validation.pdf.gz | 847.6 KB | Display | wwPDB validaton report |
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Full document | 7emu_full_validation.pdf.gz | 848.4 KB | Display | |
Data in XML | 7emu_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 7emu_validation.cif.gz | 14.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/em/7emu ftp://data.pdbj.org/pub/pdb/validation_reports/em/7emu | HTTPS FTP |
-Related structure data
Related structure data | 7emoC 7empC 7emqC 7emrC 7emsC 7emtC 7emvC 7emwC 7vm1C 3ellS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Pseudomonas aeruginosa str. PAO1 (bacteria) Gene: hasAp, PA3407 / Plasmid: pQE30 / Production host: Escherichia coli M15 (bacteria) / References: UniProt: G3XD33 |
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#2: Chemical | ChemComp-J7X / |
#3: Chemical | ChemComp-GOL / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.68 Å3/Da / Density % sol: 54.08 % / Mosaicity: 0.15 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.6 / Details: 50mM Citric acid/NaOH (pH 3.6), 10% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 26, 2019 | ||||||||||||||||||||||||
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→39.8 Å / Num. obs: 45004 / % possible obs: 99.9 % / Redundancy: 14.4 % / CC1/2: 1 / Rmerge(I) obs: 0.045 / Rpim(I) all: 0.012 / Rrim(I) all: 0.047 / Net I/σ(I): 27.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ELL Resolution: 1.35→39.8 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.762 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.053 / ESU R Free: 0.052 / 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: 81.53 Å2 / Biso mean: 25.636 Å2 / Biso min: 14.78 Å2
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Refinement step | Cycle: final / Resolution: 1.35→39.8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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