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Yorodumi- PDB-1ag9: FLAVODOXINS THAT ARE REQUIRED FOR ENZYME ACTIVATION: THE STRUCTUR... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ag9 | ||||||
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Title | FLAVODOXINS THAT ARE REQUIRED FOR ENZYME ACTIVATION: THE STRUCTURE OF OXIDIZED FLAVODOXIN FROM ESCHERICHIA COLI AT 1.8 ANGSTROMS RESOLUTION. | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / REDUCTIVE ACTIVATION / FLAVODOXIN / ESCHERICHIA COLI | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Hoover, D.M. / Ludwig, M.L. | ||||||
Citation | Journal: Protein Sci. / Year: 1997 Title: A flavodoxin that is required for enzyme activation: the structure of oxidized flavodoxin from Escherichia coli at 1.8 A resolution. Authors: 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 | 1ag9.cif.gz | 91.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ag9.ent.gz | 72 KB | Display | PDB format |
PDBx/mmJSON format | 1ag9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ag/1ag9 ftp://data.pdbj.org/pub/pdb/validation_reports/ag/1ag9 | HTTPS FTP |
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-Related structure data
Related structure data | 1ahnC 1ofvS 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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.814775, -0.137628, -0.563206), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19623.674 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: DHALPHA / Cellular location: CYTOPLASM / Gene: FLDA / Plasmid: PDH01 / Production host: Escherichia coli (E. coli) / References: UniProt: P61949 |
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-Non-polymers , 6 types, 368 molecules
#2: Chemical | ChemComp-CA / #3: Chemical | #4: Chemical | ChemComp-NA / #5: Chemical | #6: Chemical | #7: 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: 2.2 Å3/Da / Density % sol: 44.1 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 295 K / pH: 7 Details: PROTEIN WAS CRYSTALLIZED BY MICROSEEDING IN 40% MPD, 100 MM CACL2, 20 MM BIS-TRIS, 10 MM IMIDAZOLE, PH 7.0, 295 K. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion, hanging drop / Details: microseeding | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 140 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: XUONG-HAMLIN MULTIWIRE / Detector: AREA DETECTOR / Date: Dec 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→35 Å / Num. obs: 32752 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.072 / Net I/σ(I): 26.3 |
Reflection shell | Resolution: 1.8→1.88 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 5.9 / Rsym value: 0.166 / % possible all: 93.4 |
Reflection | *PLUS Num. measured all: 213264 / Rmerge(I) obs: 0.072 |
Reflection shell | *PLUS % possible obs: 93.4 % / Rmerge(I) obs: 0.166 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OFV Resolution: 1.8→10 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Cross valid method: A POSTERIORI / σ(F): 0 Details: RESIDUES 170 - 176 ARE PARTIALLY DISORDERED AND WERE MODELED USING INFORMATION FROM A DIFFERENT CRYSTAL FORM OF A HIS-TAGGED MUTANT.
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Displacement parameters | Biso mean: 25 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.8→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.88 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor all: 0.202 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor obs: 0.261 |