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Yorodumi- PDB-3jqq: Crystal structure of the H286K mutant of Ferredoxin-NADP+ reducta... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3jqq | ||||||
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Title | Crystal structure of the H286K mutant of Ferredoxin-NADP+ reductase from Plasmodium falciparum in complex with 2'P-AMP | ||||||
Components | Ferredoxin NADP reductase | ||||||
Keywords | OXIDOREDUCTASE / Ferredoxin-NADP+ reductase / FAD | ||||||
Function / homology | Function and homology information ferredoxin-NAD(P) reductase activity / regulation of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / apicoplast / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / FAD binding / electron transfer activity / identical protein binding Similarity search - Function | ||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Canevari, G. / Milani, M. / Bolognesi, M. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Plasmodium falciparum ferredoxin-NADP+ reductase His286 plays a dual role in NADP(H) binding and catalysis Authors: Crobu, D. / Canevari, G. / Milani, M. / Pandini, V. / Vanoni, M.A. / Bolognesi, M. / Zanetti, G. / Aliverti, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3jqq.cif.gz | 367.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jqq.ent.gz | 297.8 KB | Display | PDB format |
PDBx/mmJSON format | 3jqq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jqq_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 3jqq_full_validation.pdf.gz | 4.2 MB | Display | |
Data in XML | 3jqq_validation.xml.gz | 79.2 KB | Display | |
Data in CIF | 3jqq_validation.cif.gz | 107.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jq/3jqq ftp://data.pdbj.org/pub/pdb/validation_reports/jq/3jqq | HTTPS FTP |
-Related structure data
Related structure data | 3jqpC 3jqrC 2ok7S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 37307.023 Da / Num. of mol.: 6 / Fragment: residues in UNP 56-371 / Mutation: H286K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Strain: 3D7 / Gene: PfFNR, PFF1115w / Plasmid: pET-PfFNR-H286K / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: C6KT68, ferredoxin-NADP+ reductase #2: Chemical | ChemComp-FAD / #3: Chemical | ChemComp-A2P / #4: 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: 2.67 Å3/Da / Density % sol: 53.98 % |
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Crystal grow | Temperature: 293 K / Method: microbatch with permeable oil / pH: 5.4 Details: 20% isopropanol, 20% PEG 4000, 0.1M citrate-NaOH, 2mM 2'P-AMP(Cocrystallization), pH 5.4, Microbatch with permeable oil, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.1→83.918 Å / Num. all: 117739 / Num. obs: 117739 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 9.9 |
Reflection shell | Resolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.564 / Mean I/σ(I) obs: 1.8 / Num. unique all: 17208 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2OK7 Resolution: 2.2→62.12 Å / Cor.coef. Fo:Fc: 0.911 / Cor.coef. Fo:Fc free: 0.873 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.303 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.724 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→62.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.257 Å / Total num. of bins used: 20
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