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Yorodumi- PDB-7tbc: Crystal structure of Plasmepsin X from Plasmodium falciparum in c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7tbc | ||||||
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Title | Crystal structure of Plasmepsin X from Plasmodium falciparum in complex with WM382 | ||||||
Components | Plasmepsin 10 | ||||||
Keywords | HYDROLASE / Aspartyl Protease | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.76 Å | ||||||
Authors | Christensen, J.B. / Hodder, A.N. / Scally, S.W. / Cowman, A.F. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Structure / Year: 2022 Title: Basis for drug selectivity of plasmepsin IX and X inhibition in Plasmodium falciparum and vivax. Authors: Hodder, A.N. / Christensen, J. / Scally, S. / Triglia, T. / Ngo, A. / Birkinshaw, R.W. / Bailey, B. / Favuzza, P. / Dietrich, M.H. / Tham, W.H. / Czabotar, P.E. / Lowes, K. / Guo, Z. / ...Authors: Hodder, A.N. / Christensen, J. / Scally, S. / Triglia, T. / Ngo, A. / Birkinshaw, R.W. / Bailey, B. / Favuzza, P. / Dietrich, M.H. / Tham, W.H. / Czabotar, P.E. / Lowes, K. / Guo, Z. / Murgolo, N. / Lera Ruiz, M. / McCauley, J.A. / Sleebs, B.E. / Olsen, D. / Cowman, A.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tbc.cif.gz | 105.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7tbc.ent.gz | 62.6 KB | Display | PDB format |
PDBx/mmJSON format | 7tbc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tbc_validation.pdf.gz | 867.5 KB | Display | wwPDB validaton report |
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Full document | 7tbc_full_validation.pdf.gz | 869.1 KB | Display | |
Data in XML | 7tbc_validation.xml.gz | 14.4 KB | Display | |
Data in CIF | 7tbc_validation.cif.gz | 19.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tb/7tbc ftp://data.pdbj.org/pub/pdb/validation_reports/tb/7tbc | HTTPS FTP |
-Related structure data
Related structure data | 7tbbSC 7tbdC 7tbeC 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
-Protein / Sugars , 2 types, 2 molecules A
#1: Protein | Mass: 42948.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q2KNW6 |
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#3: Sugar | ChemComp-NAG / |
-Non-polymers , 4 types, 26 molecules
#2: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-PG4 / | #5: Chemical | ChemComp-I0L / ( | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 4.75 Å3/Da / Density % sol: 74.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.1M bicine-tris pH 8.5, 2.85% (v/v) diethylene glycol, 6.35% (v/v) pentaethylene glycol, 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene ...Details: 12.5% (v/v) 2-methyl-2,4-pentanediol, 0.1M bicine-tris pH 8.5, 2.85% (v/v) diethylene glycol, 6.35% (v/v) pentaethylene glycol, 12.5% (w/v) polyethylene glycol 1000, 12.5% (w/v) polyethylene glycol 3350, 5.2% (v/v) tetraethylene glycol, 4.1% (v/v) triethylene glycol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 15, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95373 Å / Relative weight: 1 |
Reflection | Resolution: 2.76→49.63 Å / Num. obs: 21289 / % possible obs: 99 % / Redundancy: 22.6 % / Biso Wilson estimate: 96.22 Å2 / CC1/2: 0.999 / Rpim(I) all: 0.03 / Net I/σ(I): 12.5 |
Reflection shell | Resolution: 2.76→2.91 Å / Redundancy: 6.5 % / Num. unique obs: 2860 / CC1/2: 0.936 / Rpim(I) all: 0.496 / % possible all: 93.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7TBB Resolution: 2.76→49.62 Å / SU ML: 0.3746 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.7843 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.76→49.62 Å
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Refine LS restraints |
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LS refinement shell |
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