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Yorodumi- PDB-2bmw: Ferredoxin: NADP+ Reductase Mutant With Thr 155 Replaced By Gly, ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2bmw | ||||||
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Title | Ferredoxin: NADP+ Reductase Mutant With Thr 155 Replaced By Gly, Ala 160 Replaced By Thr, Leu 263 Replaced By Pro, Arg 264 Replaced By Pro and Gly 265 Replaced by Pro (T155G-A160T-L263P-R264P-G265P) | ||||||
Components | FERREDOXIN--NADP REDUCTASE | ||||||
Keywords | OXIDOREDUCTASE / FLAVOPROTEIN / NADP / FAD / FNR / REDUCTASE REDUCTASE / PHYCOBILISOME / THYLAKOID | ||||||
Function / homology | Function and homology information ferredoxin-NADP+ reductase / ferredoxin-NADP+ reductase activity / phycobilisome / plasma membrane-derived thylakoid membrane / electron transport chain / NADP binding / flavin adenine dinucleotide binding Similarity search - Function | ||||||
Biological species | ANABAENA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Martinez-Julvez, M. / Hermoso, J.A. / Perez-Dorado, I. / Medina, M. / Tejero, J. / Gomez-Moreno, C. | ||||||
Citation | Journal: Biochemistry / Year: 2009 Title: Protein Motifs Involved in Coenzyme Interaction and Enzymatic Efficiency in Anabaena Ferredoxin-Nadp+ Reductase. Authors: Peregrina, J.R. / Herguedas, B. / Hermoso, J.A. / Martinez-Julvez, M. / Medina, M. #1: Journal: Biophys.Chem. / Year: 2005 Title: Towards a New Therapeutic Target: Helicobacter Pylori Flavodoxin Authors: Cremades, N. / Bueno, M. / Toja, M. / Sancho, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bmw.cif.gz | 88.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bmw.ent.gz | 64.9 KB | Display | PDB format |
PDBx/mmJSON format | 2bmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/2bmw ftp://data.pdbj.org/pub/pdb/validation_reports/bm/2bmw | HTTPS FTP |
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-Related structure data
Related structure data | 2vyqC 2vzlC 1queS 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 34122.781 Da / Num. of mol.: 1 / Fragment: RESIDUES 137-440 / Mutation: YES Source method: isolated from a genetically manipulated source Details: MUTATIONS T155G, A160T, L263P, R264P AND G265P / Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase |
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#2: Chemical | ChemComp-FAD / |
#3: Chemical | ChemComp-SO4 / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.66 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM16 / Wavelength: 0.97954 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 2, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97954 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→29.5 Å / Num. obs: 64511 / % possible obs: 99.9 % / Observed criterion σ(I): 6 / Redundancy: 8.9 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.1 / Rsym value: 0.1 / Net I/σ(I): 14.5 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.3 / Rsym value: 0.32 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1QUE Resolution: 1.5→28.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1616756 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: THE FIRST 8 RESIDUES WERE NOT FOUND IN THE ELECTRONIC DENSITY
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.4346 Å2 / ksol: 0.337619 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.1 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.5→28.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.59 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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