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Yorodumi- PDB-6hl7: Crystal structure of truncated aspartate transcarbamoylase from P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hl7 | |||||||||
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Title | Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum with mutated active site (R109A/K138A) and N-carbamoyl-L-phosphate bound | |||||||||
Components | Aspartate transcarbamoylaseAspartate carbamoyltransferase | |||||||||
Keywords | TRANSFERASE / Falciparum Malaria Pyrimidine biosynthesis Trimer Mutant TRANSFERASE carbamoyl-phospahte | |||||||||
Function / homology | Function and homology information aspartate carbamoyltransferase / aspartate carbamoyltransferase activity / amino acid metabolic process / amino acid binding / 'de novo' UMP biosynthetic process / 'de novo' pyrimidine nucleobase biosynthetic process / membrane Similarity search - Function | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Bosch, S.S. / Lunev, S. / Wrenger, C. / Groves, M.R. | |||||||||
Funding support | Brazil, 2items
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Citation | Journal: Acs Infect Dis. / Year: 2020 Title: Molecular Target Validation of Aspartate Transcarbamoylase fromPlasmodium falciparumby Torin 2. Authors: Bosch, S.S. / Lunev, S. / Batista, F.A. / Linzke, M. / Kronenberger, T. / Domling, A.S.S. / Groves, M.R. / Wrenger, C. #1: Journal: Acta Crystallogr F Struct Biol Commun / Year: 2016 Title: Crystal structure of truncated aspartate transcarbamoylase from Plasmodium falciparum. Authors: Lunev, S. / Bosch, S.S. / de Assis Batista, F. / Wrenger, C. / Groves, M.R. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hl7.cif.gz | 205.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hl7.ent.gz | 165 KB | Display | PDB format |
PDBx/mmJSON format | 6hl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/6hl7 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/6hl7 | HTTPS FTP |
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-Related structure data
Related structure data | 5ilqS 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: 40119.465 Da / Num. of mol.: 3 / Mutation: R109A, K138A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: ATCase / Production host: Escherichia coli (E. coli) / References: UniProt: O15804, aspartate carbamoyltransferase #2: Chemical | #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: 3.06 Å3/Da / Density % sol: 59.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2M Potassium citrate tribasic monohydrate 20% w/v PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 3, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→57.61 Å / Num. obs: 46404 / % possible obs: 97.6 % / Observed criterion σ(I): 1.3 / Redundancy: 3.16 % / CC1/2: 0.999 / Rrim(I) all: 0.066 / Net I/σ(I): 12.95 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 3.21 % / Num. unique obs: 7154 / CC1/2: 0.619 / Rrim(I) all: 0.957 / % possible all: 94 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5ilq Resolution: 2.5→57.61 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.432 / ESU R Free: 0.283 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 163.5 Å2 / Biso mean: 65.452 Å2 / Biso min: 28.67 Å2
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Refinement step | Cycle: final / Resolution: 2.5→57.61 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.502→2.567 Å / Total num. of bins used: 20
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