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Yorodumi- PDB-6kuc: Crystal structure of Plasmodium falciparum histo-aspartic proteas... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6kuc | ||||||
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Title | Crystal structure of Plasmodium falciparum histo-aspartic protease (HAP) zymogen (Form 2) | ||||||
Components | HAP protein | ||||||
Keywords | HYDROLASE / Histo-Aspartic protease / HAP / Plasmepsin / Proplasmepsin / Zymogen / Aspartic Protease | ||||||
Function / homology | Function and homology information plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / aspartic-type endopeptidase activity / proteolysis / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Rathore, I. / Mishra, V. / Bhaumik, P. | ||||||
Funding support | India, 1items
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Citation | Journal: Febs J. / Year: 2021 Title: Activation mechanism of plasmepsins, pepsin-like aspartic proteases from Plasmodium, follows a unique trans-activation pathway. Authors: Rathore, I. / Mishra, V. / Patel, C. / Xiao, H. / Gustchina, A. / Wlodawer, A. / Yada, R.Y. / Bhaumik, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6kuc.cif.gz | 165.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6kuc.ent.gz | 135.9 KB | Display | PDB format |
PDBx/mmJSON format | 6kuc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6kuc_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 6kuc_full_validation.pdf.gz | 465.9 KB | Display | |
Data in XML | 6kuc_validation.xml.gz | 17.6 KB | Display | |
Data in CIF | 6kuc_validation.cif.gz | 24.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ku/6kuc ftp://data.pdbj.org/pub/pdb/validation_reports/ku/6kuc | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43048.777 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: hap / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: Q9Y006 | ||||||
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#2: Chemical | ChemComp-PEG / #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.46 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop Details: 0.2M Lithium citrate tribasic tetrahydrate, 20% w/v Polyethylene glycol 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 30, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→36.5 Å / Num. obs: 17267 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.12 |
Reflection shell | Resolution: 2.5→2.6 Å / Rmerge(I) obs: 1.6 / Mean I/σ(I) obs: 1.2 / Num. unique obs: 1890 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→36.5 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.93 / SU B: 28.288 / SU ML: 0.288 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.46 / ESU R Free: 0.28 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 132.62 Å2 / Biso mean: 63.264 Å2 / Biso min: 31.13 Å2
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Refinement step | Cycle: final / Resolution: 2.5→36.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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