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Yorodumi- PDB-2xnc: Crystal structure of an engineered Ferredoxin NADP reductase (FNR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xnc | ||||||
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Title | Crystal structure of an engineered Ferredoxin NADP reductase (FNR) from Pisum sativum | ||||||
Components | FERREDOXIN--NADP REDUCTASE, LEAF ISOZYME, CHLOROPLASTIC | ||||||
Keywords | OXIDOREDUCTASE / CHLOROPLAST / FLAVOPROTEIN / TRANSPORT / PHOTOSYNTHESIS / ELECTRON TRANSPORT | ||||||
Function / homology | Function and homology information chloroplast thylakoid membrane protein complex / ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / NADPH dehydrogenase activity / chloroplast stroma / photosynthesis / electron transport chain Similarity search - Function | ||||||
Biological species | PISUM SATIVUM (garden pea) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Botti, H. / Musumeci, M.A. / Ceccarelli, E.A. / Buschiazzo, A. | ||||||
Citation | Journal: Biochemistry / Year: 2011 Title: Swapping Fad Binding Motifs between Plastidic and Bacterial Ferredoxin-Nadp(H) Reductases. Authors: Musumeci, M.A. / Botti, H. / Buschiazzo, A. / Ceccarelli, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2xnc.cif.gz | 253.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xnc.ent.gz | 207.7 KB | Display | PDB format |
PDBx/mmJSON format | 2xnc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xnc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2xnc_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 2xnc_validation.xml.gz | 22.9 KB | Display | |
Data in CIF | 2xnc_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xn/2xnc ftp://data.pdbj.org/pub/pdb/validation_reports/xn/2xnc | HTTPS FTP |
-Related structure data
Related structure data | 2xnjC 1qg0S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 35569.934 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Details: THE LOOP BETWEEN WILD-TYPE RESIDUES 115-123 (INCLUSIVE) HAS BEEN DELETED AND A C-TERMINAL TRP HAS BEEN INSERTED (W300) Source: (gene. exp.) PISUM SATIVUM (garden pea) / Plasmid: PET32B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS / References: UniProt: P10933, ferredoxin-NADP+ reductase #2: Chemical | #3: Chemical | ChemComp-SO4 / #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: 2.58 Å3/Da / Density % sol: 52.35 % / Description: NONE |
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Crystal grow | pH: 8 / Details: pH 8 |
-Data collection
Diffraction | Mean temperature: 108 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: VARIMAX-HF MIRRORS |
Radiation | Monochromator: VARIMAX-HF MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→28.9 Å / Num. obs: 18774 / % possible obs: 99.7 % / Observed criterion σ(I): 1 / Redundancy: 4.6 % / Biso Wilson estimate: 73.98 Å2 / Rmerge(I) obs: 0.09 / Rsym value: 0.09 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.9→3.06 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.9 / Rsym value: 0.53 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QG0 Resolution: 2.9→28.04 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 90.81 Å2
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Refine analyze | Luzzati coordinate error obs: 0.5 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→28.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.08 Å / Total num. of bins used: 9
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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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