+Open data
-Basic information
Entry | Database: PDB / ID: 1jig | ||||||
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Title | Dlp-2 from Bacillus anthracis | ||||||
Components | Dlp-2 | ||||||
Keywords | METAL TRANSPORT / dodecamer / four-helix bundle | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / oxidoreductase activity, acting on metal ions / ferric iron binding / intracellular iron ion homeostasis / cytoplasm Similarity search - Function | ||||||
Biological species | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.46 Å | ||||||
Authors | Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2002 Title: Structure of two iron-binding proteins from Bacillus anthracis. Authors: Papinutto, E. / Dundon, W.G. / Pitulis, N. / Battistutta, R. / Montecucco, C. / Zanotti, G. #1: Journal: Nat.Struct.Biol. / Year: 1998 Title: The Crystal Structure of Dps, a Ferritin Homolog that Binds and Protects DNA Authors: Grant, R.A. / Filman, D.J. / Finkel, S.E. / Kolter, R. / Hogle, J.M. #2: Journal: Nat.Struct.Biol. / Year: 2000 Title: The Dodecameric Ferritin from Listeria innocua Contains a Novel Intersubunit Iron-binding Site Authors: Ilari, A. / Stefanini, S. / Chiancone, E. / Tsernoglou, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1jig.cif.gz | 129.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1jig.ent.gz | 102.2 KB | Display | PDB format |
PDBx/mmJSON format | 1jig.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jig_validation.pdf.gz | 460 KB | Display | wwPDB validaton report |
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Full document | 1jig_full_validation.pdf.gz | 498.1 KB | Display | |
Data in XML | 1jig_validation.xml.gz | 30.5 KB | Display | |
Data in CIF | 1jig_validation.cif.gz | 41.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ji/1jig ftp://data.pdbj.org/pub/pdb/validation_reports/ji/1jig | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | The biological assembly is a dodecamer generated from the tetramer in the asymmetric unit by the operations: -y, x-y, z and -x+y, -x, z. |
-Components
#1: Protein | Mass: 16533.580 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: dlp-2 / Plasmid: pSM214G / Production host: Escherichia coli (E. coli) / Strain (production host): XL1-blue / References: UniProt: Q8RPQ1 #2: Chemical | ChemComp-FE / #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: 2.76 Å3/Da / Density % sol: 55 % | ||||||||||||||||||||||||
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: Citrete buffer, ammonuium acetate, MPD, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.93 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 8, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.46→50 Å / Num. all: 105192 / Num. obs: 105192 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.032 / Net I/σ(I): 12.7 |
Reflection shell | Resolution: 1.46→1.54 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9 / Num. unique all: 13823 / % possible all: 88.2 |
Reflection | *PLUS Lowest resolution: 50 Å / Redundancy: 3 % / Rmerge(I) obs: 0.032 |
Reflection shell | *PLUS % possible obs: 88.2 % / Num. unique obs: 13823 / Rmerge(I) obs: 0.068 / Mean I/σ(I) obs: 9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: HP-NAP Resolution: 1.46→71.63 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2406290.76 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 Details: The crystal presents a nearly perfect twinning. The refinement was carried on with the twinning procedure of CNS, with the twinning law h,-h-k,-l.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 58.65 Å2 / ksol: 0.443 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.5 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.46→71.63 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR / Rms dev position: 0.016 Å / Weight Biso : 4 / Weight position: 300 | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.46→1.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS Lowest resolution: 50 Å / Rfactor obs: 0.186 / Rfactor Rfree: 0.205 / Rfactor Rwork: 0.186 | ||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.231 / Rfactor Rwork: 0.224 / Rfactor obs: 0.224 |