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Yorodumi- PDB-1d03: REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS -
+Open data
-Basic information
Entry | Database: PDB / ID: 1d03 | ||||||
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Title | REFINED STRUCTURES OF OXIDIZED FLAVODOXIN FROM ANACYSTIS NIDULANS | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / FLAVODOXIN / FMN BINDING / REDOX POTENTIAL | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Synechococcus elongatus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.85 Å | ||||||
Authors | Drennan, C.L. / Pattridge, K.A. / Weber, C.H. / Metzger, A.L. / Hoover, D.M. / Ludwig, M.L. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1999 Title: Refined structures of oxidized flavodoxin from Anacystis nidulans. Authors: Drennan, C.L. / Pattridge, K.A. / Weber, C.H. / Metzger, A.L. / Hoover, D.M. / Ludwig, M.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1d03.cif.gz | 49.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1d03.ent.gz | 35.2 KB | Display | PDB format |
PDBx/mmJSON format | 1d03.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d0/1d03 ftp://data.pdbj.org/pub/pdb/validation_reports/d0/1d03 | HTTPS FTP |
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-Related 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: 18599.244 Da / Num. of mol.: 1 / Mutation: N58G Source method: isolated from a genetically manipulated source Details: OXIDIZED / Source: (gene. exp.) Synechococcus elongatus (bacteria) / Strain: PCC 7942 / Plasmid: PKK233-2-ANFLD / Production host: Escherichia coli (E. coli) / Strain (production host): W1485 / References: UniProt: P10340 |
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#2: Chemical | ChemComp-FMN / |
#3: 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: 3.85 Å3/Da / Density % sol: 68.06 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: AMMONIUM SULFATE, POTASSIUM PHOSPHATE, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Details: used to seeding | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: SDMS / Detector: AREA DETECTOR / Date: Jun 27, 1991 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Biso Wilson estimate: 12.7 Å2 |
Reflection shell | Resolution: 1.9→1.99 Å / Num. unique all: 2229 / % possible all: 78.4 |
Reflection | *PLUS Highest resolution: 1.85 Å / Lowest resolution: 10 Å / Num. obs: 21005 / % possible obs: 84 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.047 |
Reflection shell | *PLUS % possible obs: 78 % |
-Processing
Software |
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Refinement | Resolution: 1.85→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: A POSTERIORI / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 18.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.85→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.97 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
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Xplor file |
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Software | *PLUS Name: X-PLOR(ONLINE) / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS σ(F): 0 / % reflection Rfree: 10 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 18.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.224 / % reflection Rfree: 10.4 % / Rfactor Rwork: 0.206 |