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Yorodumi- PDB-1tjo: Iron-oxo clusters biomineralizing on protein surfaces. Structural... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1tjo | ||||||
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Title | Iron-oxo clusters biomineralizing on protein surfaces. Structural analysis of H.salinarum DpsA in its low and high iron states | ||||||
Components | Iron-rich dpsA-homolog protein | ||||||
Keywords | METAL BINDING PROTEIN / DpsA / ferritin / low-iron | ||||||
Function / homology | Function and homology information Oxidoreductases; Oxidizing metal ions / ferric iron binding / intracellular iron ion homeostasis / oxidoreductase activity / cytoplasm Similarity search - Function | ||||||
Biological species | Halobacterium salinarum (Halophile) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Zeth, K. / Offermann, S. / Essen, L.O. / Oesterhelt, D. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2004 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1tjo.cif.gz | 168.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1tjo.ent.gz | 132.1 KB | Display | PDB format |
PDBx/mmJSON format | 1tjo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1tjo_validation.pdf.gz | 404.6 KB | Display | wwPDB validaton report |
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Full document | 1tjo_full_validation.pdf.gz | 419.1 KB | Display | |
Data in XML | 1tjo_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 1tjo_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tj/1tjo ftp://data.pdbj.org/pub/pdb/validation_reports/tj/1tjo | HTTPS FTP |
-Related structure data
Related structure data | 1mojC 1tk6C 1tkoC 1tkpC 1dpsS C: citing same article (ref.) 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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Components on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 4 / Auth seq-ID: 7 - 181 / Label seq-ID: 7 - 181
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Details | The protein is dodecameric with a tetramer in the AU. The dodecamer can be constructed by simple crystallographic operations. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 20121.846 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Halobacterium salinarum (Halophile) / Strain: wildtype strain - TOM / References: UniProt: Q9HMP7 |
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-Non-polymers , 5 types, 810 molecules
#2: Chemical | #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-MG / #5: Chemical | #6: 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: 2.1 Å3/Da / Density % sol: 42 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG400, 1M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.93 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 3, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.93 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→158 Å / Num. obs: 92251 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 5.5 % / Biso Wilson estimate: 28.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 10 |
Reflection shell | Resolution: 1.6→1.641 Å / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: Dps-protein from E. coli - PDB entry 1DPS Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.945 / SU B: 1.793 / SU ML: 0.061 / Cross valid method: THROUGHOUT / σ(I): 0 / ESU R: 0.086 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.515 Å2
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Refine analyze | Luzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.21 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→15 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 2553 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.6→1.641 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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