+Open data
-Basic information
Entry | Database: PDB / ID: 1qfz | ||||||
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Title | PEA FNR Y308S MUTANT IN COMPLEX WITH NADPH | ||||||
Components | PROTEIN (FERREDOXIN:NADP+ REDUCTASE) | ||||||
Keywords | OXIDOREDUCTASE / FLAVOENZYME / PHOTOSYNTHESIS / ELECTRON TRANSFER / HYDRIDE TRANSFER | ||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Deng, Z. / Aliverti, A. / Zanetti, G. / Arakaki, A.K. / Ottado, J. / Orellano, E.G. / Calcaterra, N.B. / Ceccarelli, E.A. / Carrillo, N. / Karplus, P.A. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1999 Title: A productive NADP+ binding mode of ferredoxin-NADP+ reductase revealed by protein engineering and crystallographic studies. Authors: Deng, Z. / Aliverti, A. / Zanetti, G. / Arakaki, A.K. / Ottado, J. / Orellano, E.G. / Calcaterra, N.B. / Ceccarelli, E.A. / Carrillo, N. / Karplus, P.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1qfz.cif.gz | 155.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1qfz.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 1qfz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1qfz_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 1qfz_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 1qfz_validation.xml.gz | 35.1 KB | Display | |
Data in CIF | 1qfz_validation.cif.gz | 52 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qf/1qfz ftp://data.pdbj.org/pub/pdb/validation_reports/qf/1qfz | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.986029, -0.044485, -0.160521), Vector: |
-Components
#1: Protein | Mass: 34767.969 Da / Num. of mol.: 2 / Mutation: Y308S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pisum sativum (garden pea) / Organ: LEAF / Production host: Escherichia coli (E. coli) / References: UniProt: P10933, ferredoxin-NADP+ reductase #2: Chemical | ChemComp-SO4 / | #3: Chemical | #4: Chemical | #5: 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: 3.3 Å3/Da / Density % sol: 62 % | |||||||||||||||||||||||||
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Crystal grow | pH: 8 / Details: pH 8.0 | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 25 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
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: CHESS / Beamline: F1 / Wavelength: 0.91 |
Detector | Detector: CCD / Date: Feb 1, 1998 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→30 Å / Num. obs: 92562 / % possible obs: 96.1 % / Redundancy: 3.9 % / Rsym value: 0.052 / Net I/σ(I): 9 |
Reflection shell | Resolution: 1.7→1.79 Å / Redundancy: 3 % / Mean I/σ(I) obs: 2.4 / Rsym value: 0.279 / % possible all: 90.6 |
Reflection | *PLUS Num. measured all: 357117 / Rmerge(I) obs: 0.058 |
Reflection shell | *PLUS % possible obs: 90.6 % / Rmerge(I) obs: 0.334 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Y308S:NADP+ Resolution: 1.7→8 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters | Biso mean: 27 Å2
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Refinement step | Cycle: LAST / Resolution: 1.7→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.7→1.78 Å / Total num. of bins used: 8
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.7 Å / Lowest resolution: 8 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.201 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 27 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.7 Å / Rfactor Rfree: 0.37 / % reflection Rfree: 5 % / Rfactor Rwork: 0.359 |