+Open data
-Basic information
Entry | Database: PDB / ID: 1dx9 | ||||||
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Title | W57A Apoflavodoxin from Anabaena | ||||||
Components | Flavodoxin | ||||||
Keywords | FLAVOPROTEIN | ||||||
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 | Nostoc sp. (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
Authors | Romero, A. / Sancho, J. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Dissecting the Energetics of the Apoflavodoxin-Fmn Complex Authors: Lostao, A. / El-Harrous, M. / Daoudi, F. / Romero, A. / Parody-Morreale, A. / Sancho, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1dx9.cif.gz | 144.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1dx9.ent.gz | 114.3 KB | Display | PDB format |
PDBx/mmJSON format | 1dx9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1dx9_validation.pdf.gz | 459.8 KB | Display | wwPDB validaton report |
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Full document | 1dx9_full_validation.pdf.gz | 464.7 KB | Display | |
Data in XML | 1dx9_validation.xml.gz | 27.6 KB | Display | |
Data in CIF | 1dx9_validation.cif.gz | 38.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dx/1dx9 ftp://data.pdbj.org/pub/pdb/validation_reports/dx/1dx9 | HTTPS FTP |
-Related structure data
Related structure data | 1ftgS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 18732.396 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) Nostoc sp. (strain ATCC 29151 / PCC 7119) (bacteria) Strain: ATCC 29151 / PCC 7119 / Cell line: E.COLI JM109 / Gene: isiB / Plasmid: PTRC99A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TG1 / References: UniProt: P0A3E0 #2: Chemical | ChemComp-SO4 / #3: 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: 1.96 Å3/Da / Density % sol: 37 % | ||||||||||||||||||||
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Crystal grow | pH: 6 Details: 3.2 M AMMONIUM SULPHATE, 100 MM NA.K-PHOSPHATE, PH 6.0. PROTEIN CONCENTRATION 16 MG/ML | ||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion | ||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 15, 1999 |
Radiation | Monochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→20 Å / Num. obs: 36277 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 17.138 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.0584 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.05→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.074 / Mean I/σ(I) obs: 13.3 / % possible all: 97 |
Reflection | *PLUS % possible obs: 93 % / Num. measured all: 129267 / Rmerge(I) obs: 0.041 |
Reflection shell | *PLUS % possible obs: 94.4 % / Rmerge(I) obs: 0.065 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1FTG Resolution: 2.05→8 Å / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: THE N-TERMINAL SER RESIDUE COULD NOT BE MODELLED INTO THE ELECTRON DENSITY MAP, AS THERE ARE NO DENSITY FOR THIS RESIDUE.
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Displacement parameters | Biso mean: 17.864 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.05→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.05→2.14 Å / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.16 / Rfactor Rfree: 0.256 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 17.864 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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