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Yorodumi- PDB-1jym: Crystals of Peptide Deformylase from Plasmodium falciparum with T... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1jym | ||||||
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Title | Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design | ||||||
Components | Peptide Deformylase | ||||||
Keywords | HYDROLASE / PDF / malaria / plasmodium / deformylation / metalloenzyme | ||||||
Function / homology | Function and homology information apicoplast / co-translational protein modification / N-terminal protein amino acid modification / peptide deformylase / peptide deformylase activity / ferrous iron binding / translation / mitochondrion / membrane Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å | ||||||
Authors | Kumar, A. / Nguyen, K.T. / Srivathsan, S. / Ornstein, B. / Turley, S. / Hirsh, I. / Pei, D. / Hol, W.G.J. | ||||||
Citation | Journal: Structure / Year: 2002 Title: Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design. Authors: Kumar, A. / Nguyen, K.T. / Srivathsan, S. / Ornstein, B. / Turley, S. / Hirsh, I. / Pei, D. / Hol, W.G. #1: Journal: Protein Sci. / Year: 2004 Title: An improved crystal form of Plasmodium falciparum peptide deformylase Authors: Robien, M.A. / Nguyen, K.T. / Kumar, A. / Hirsh, I. / Turley, S. / Pei, D. / Hol, W.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jym.cif.gz | 363.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jym.ent.gz | 300 KB | Display | PDB format |
PDBx/mmJSON format | 1jym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jy/1jym ftp://data.pdbj.org/pub/pdb/validation_reports/jy/1jym | HTTPS FTP |
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-Related structure data
Related structure data | 1dffS S: Starting model for refinement |
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Similar 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: 21821.820 Da / Num. of mol.: 10 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: PDF / Plasmid: pET29b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8I372, EC: 3.5.1.31 #2: Chemical | ChemComp-CO / #3: Water | ChemComp-HOH / | |
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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: 3 Å3/Da / Density % sol: 55 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Tris, Sodium chloride, Magnesium chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97918, 0.97938, 0.96396 | ||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: May 5, 2001 | ||||||||||||
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 2.8→30 Å / Num. all: 62948 / Num. obs: 51866 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rsym value: 0.101 | ||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Rsym value: 0.594 / % possible all: 97.1 | ||||||||||||
Reflection | *PLUS Num. obs: 62948 / Rmerge(I) obs: 0.101 | ||||||||||||
Reflection shell | *PLUS % possible obs: 97.1 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
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Refinement | Method to determine structure: MAD Starting model: PDB ENTRY 1DFF Resolution: 2.8→30 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.826 / SU B: 21.435 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.489 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 49.586 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.9 Å / Total num. of bins used: 20 /
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Refinement | *PLUS σ(F): 2 / % reflection Rfree: 5.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / Rfactor Rwork: 0.272 |