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- PDB-1moj: Crystal structure of an archaeal dps-homologue from Halobacterium... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1moj | ||||||
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Title | Crystal structure of an archaeal dps-homologue from Halobacterium salinarum | ||||||
![]() | Dps-like ferritin | ||||||
![]() | DNA BINDING PROTEIN / dps / ferritin / four-helix bundle / halophilic | ||||||
Function / homology | ![]() Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zeth, K. / Offermann, S. / Essen, L.O. / Oesterhelt, D. | ||||||
![]() | ![]() Title: Iron-oxo clusters biomineralizing on protein surfaces: Structural analysis of Halobacterium salinarum DpsA in its low- and high-iron states. Authors: Zeth, K. / Offermann, S. / Essen, L.O. / Oesterhelt, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 150.4 KB | Display | ![]() |
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PDB format | ![]() | 119.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 446.2 KB | Display | ![]() |
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Full document | ![]() | 454.9 KB | Display | |
Data in XML | ![]() | 28.1 KB | Display | |
Data in CIF | ![]() | 39.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1tjoC ![]() 1tk6C ![]() 1tkoC ![]() 1tkpC ![]() 1dpsS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Details | The biological assembly of a 23-symmetric dodecamer is generated from the tetramer in the asymmetric unit by the operations: -Y,X-Y,Z and Y-X,-X,Z |
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Components
#1: Protein | Mass: 20121.846 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() #2: Chemical | ChemComp-FE / #3: Chemical | #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.25 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8 Details: PEG 400, Tris/HCl, magnesium chloride, sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2001 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9762 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→30 Å / Num. all: 66071 / Num. obs: 63709 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 1.8→1.99 Å / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 4.1 / % possible all: 99.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1DPS Resolution: 1.9→29.88 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The crystal was merohedrally twinned along the z-axis with a twinning ratio of 0.57/0.43 for relating reflections h,k,l with -h,-k,l. Refinement of the twinned crystal proceeded in CNS, but ...Details: The crystal was merohedrally twinned along the z-axis with a twinning ratio of 0.57/0.43 for relating reflections h,k,l with -h,-k,l. Refinement of the twinned crystal proceeded in CNS, but the twinned R-factors are systematically underestimated compared to the non-twinned case
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.7172 Å2 / ksol: 0.427365 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.5 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.88 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.9→1.99 Å / Total num. of bins used: 8
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Xplor file |
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