+Open data
-Basic information
Entry | Database: PDB / ID: 2v5u | ||||||
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Title | I92A FLAVODOXIN FROM ANABAENA | ||||||
Components | FLAVODOXIN | ||||||
Keywords | ELECTRON TRANSPORT / FMN / TRANSPORT / FLAVOPROTEIN / ELECTRON TRANSFER | ||||||
Function / homology | Function and homology information cellular response to iron ion starvation / electron transport chain / FMN binding / electron transfer activity Similarity search - Function | ||||||
Biological species | ANABAENA SP. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.99 Å | ||||||
Authors | Martinez-Julvez, M. / Herguedas, B. / Frago, S. / Serrano, A. / Molina, R. / Hamiaux, C. / Schierbeek, B. / Medina, M. / Hermoso, J.A. | ||||||
Citation | Journal: Arch.Biochem.Biophys. / Year: 2007 Title: Tuning of the Fmn Binding and Oxido-Reduction Properties by Neighboring Side Chains in Anabaena Flavodoxin. Authors: Frago, S. / Goni, G. / Herguedas, B. / Peregrina, J.R. / Serrano, A. / Perez-Dorado, I. / Molina, R. / Gomez-Moreno, C. / Hermoso, J.A. / Martinez-Julvez, M. / Mayhew, S.G. / Medina, M. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2v5u.cif.gz | 85.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2v5u.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 2v5u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5u ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5u | HTTPS FTP |
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-Related structure data
Related structure data | 2v5vC 1oboS 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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-Components
#1: Protein | Mass: 18789.449 Da / Num. of mol.: 2 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) ANABAENA SP. (bacteria) / Strain: PCC 7119 / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / Variant (production host): TG1 / References: UniProt: P0A3E0 #2: Chemical | #3: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, SER 1 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 92 TO ALA ENGINEERED ...ENGINEERED | Sequence details | RECOMBINANT FLD VARIANT LACKS THE FIRST METHIONINE AND THE SECOND AMINOACID IS AN ALANINE. ...RECOMBINAN | |
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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: 2.09 Å3/Da / Density % sol: 41.08 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 30% PEG4K, 100 MM TRIS/HCL PH 8.5, 0.2 M MGCL2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 |
Detector | Type: BRUKER / Detector: CCD / Date: Mar 30, 2006 / Details: HELIOS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→26.58 Å / Num. obs: 21357 / % possible obs: 94.4 % / Redundancy: 9.91 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 20.03 |
Reflection shell | Resolution: 1.99→2.1 Å / Redundancy: 4.61 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 4.27 / % possible all: 83.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OBO Resolution: 1.99→26.13 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.892 / SU B: 6.789 / SU ML: 0.182 / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. IN CHAIN A, THERE IS NO ELECTRONIC DENSITY FOR THE FIRST TWO AMINOACIDS. IN CHAIN B, ALL AMINOACIDS ARE VISIBLE.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.48 Å2
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Refinement step | Cycle: LAST / Resolution: 1.99→26.13 Å
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Refine LS restraints |
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