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Yorodumi- PDB-1w87: FERREDOXIN-NADP REDUCTASE (MUTATION: Y 303 W) COMPLEXED WITH NADP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w87 | ||||||
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Title | FERREDOXIN-NADP REDUCTASE (MUTATION: Y 303 W) COMPLEXED WITH NADP BY COCRYSTALLIZATION | ||||||
Components | FERREDOXIN-NADP REDUCTASEFerredoxin—NADP(+) reductase | ||||||
Keywords | OXIDOREDUCTASE / FAD / FLAVOPROTEIN / FNR / NADP / NADP 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 / flavin adenine dinucleotide binding / NADP binding Similarity search - Function | ||||||
Biological species | ANABAENA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Hermoso, J.A. / Perez-Dorado, I. / Maya, C. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: C-Terminal Tyrosine of Ferredoxin-Nadp(+) Reductase in Hydride Transfer Processes with Nad(P)(+)/H. Authors: Tejero, J. / Perez-Dorado, I. / Maya, C. / Julvez, M.M. / Sanz-Aparicio, J. / Gomez-Moreno, C. / Hermoso, J.A. / Medina, M. #1: Journal: J.Mol.Biol. / Year: 2001 Title: Mechanism of Coenzyme Recognition and Binding Revealed by Crystal Structure Analysis of Ferredoxin-Nadp Reductase Complexed with Nadp Authors: Hermoso, J.A. / Mayoral, T. / Faro, M. / Gomez-Moreno, C. / Sanz-Aparicio, J. / Medina, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w87.cif.gz | 133.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w87.ent.gz | 105.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w87.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w8/1w87 ftp://data.pdbj.org/pub/pdb/validation_reports/w8/1w87 | HTTPS FTP |
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-Related structure data
Related structure data | 1w34C 1w35C 2bsaC 1gjrS 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.95783, 0.02447, 0.28628), Vector: |
-Components
#1: Protein | Mass: 34195.910 Da / Num. of mol.: 2 / Fragment: RESIDUES 137-440 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P21890, ferredoxin-NADP+ reductase #2: Chemical | #3: Chemical | Compound details | CHAIN A, B ENGINEERED | Sequence details | TYR 303 WAS MUTATED BY TRP | |
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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: 3.2 Å3/Da / Density % sol: 62 % |
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Crystal grow | pH: 5 / Details: pH 5.00 |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: ROTATING ANODE / Wavelength: 1.54179 |
Detector | Type: BRUKER-NONIUS / Detector: CCD / Date: Jul 7, 2004 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 3→34.99 Å / Num. obs: 16780 / % possible obs: 83.6 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.01 / Net I/σ(I): 3.9 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.41 / Mean I/σ(I) obs: 1.3 / % possible all: 48.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1GJR Resolution: 3→34.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 3233025.06 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: ELECTRON DENSITY WAS NOT PRESENT FOR RESIDUES 0-8.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 31.2793 Å2 / ksol: 0.374794 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 35.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3→34.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3→3.19 Å / Rfactor Rfree error: 0.037 / Total num. of bins used: 6
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Xplor file |
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