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- PDB-2oc5: Crystal structure of a ferritin-like protein (pmt1231) from proch... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2oc5 | ||||||
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Title | Crystal structure of a ferritin-like protein (pmt1231) from prochlorococcus marinus str. mit 9313 at 1.68 A resolution | ||||||
![]() | Hypothetical protein | ||||||
![]() | METAL BINDING PROTEIN / Duf3066 family protein / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | ![]() aldehyde oxygenase (deformylating) / : / : / transition metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Joint Center for Structural Genomics (JCSG) | ||||||
![]() | ![]() Title: Crystal structure of hypothetical protein (NP_895059.1) from Prochlorococcus marinus MIT9313 at 1.68 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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Remark 999 | SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS ...SEQUENCE THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. | ||||||
Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). SIZE EXCLUSION CHROMATOGRAPHY SUPPORTS THE ASSIGNMENT OF A MONOMER AS A BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.2 KB | Display | ![]() |
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PDB format | ![]() | 50.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 443.5 KB | Display | ![]() |
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Full document | ![]() | 445.2 KB | Display | |
Data in XML | ![]() | 13.9 KB | Display | |
Data in CIF | ![]() | 21.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
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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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Components
#1: Protein | Mass: 27640.135 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||||||
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#2: Chemical | #3: Chemical | ChemComp-ACT / | #4: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.16 Å3/Da / Density % sol: 61.1 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 7.8 Details: 0.2M KAcetate, 20.0% PEG-3350, No Buffer pH 7.8, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 5, 2006 / Details: Flat collimating mirror, toroid focusing mirror | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.68→29.235 Å / Num. obs: 41123 / % possible obs: 99.6 % / Biso Wilson estimate: 30.354 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 10.19 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: ![]() |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN ...Details: 1.HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2.ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 3.A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 TO ACCOUNT FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4.TWO FE ATOMS AND AN UNKNOWN LIGAND (UNL) WERE MODELED INTO ELECTRON DENISTY NEAR GLU 45, GLU 73, HIS 76 GLU 128, AND HIS 160. AN ACETATE MOLECULE FROM THE CRYSTALLIZATION WAS ALSO MODELED. THE PRESENCE OF THE TWO IRON ATOMS IS SUPPORTED BY X-RAY FLUORESCENCE MEASUREMENTS, ANOMALOUS DIFFERENCE FOURIERS AND GEOMETRY. 5.RESIDUES 1-19 AT N-TERMINAL END ARE DISORDERED AND NOT BUILT IN THIS MODEL. 6.UNEXPLAINED ELECTRON DENSITY IS LOCATED NEAR ALA 238 AND ALA 239.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.126 Å2
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Refinement step | Cycle: LAST / Resolution: 1.68→29.235 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.679→1.723 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 18.199 Å / Origin y: 36.904 Å / Origin z: 39.066 Å
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Refinement TLS group | Selection: ALL |