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Yorodumi- PDB-3ez0: Crystal structure of protein of unknown function with ferritin-li... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3ez0 | ||||||
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Title | Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution | ||||||
Components | uncharacterized protein with ferritin-like fold | ||||||
Keywords | structural genomics / unknown function / YP_832262.1 / protein of unknown function with ferritin-like fold / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Ferritin, core subunit, four-helix bundle / Ferritin / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Mainly Alpha / L(+)-TARTARIC ACID / Unknown ligand / Uncharacterized protein Function and homology information | ||||||
Biological species | Arthrobacter sp. FB24 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.33 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of protein of unknown function with ferritin-like fold (YP_832262.1) from Arthrobacter sp. FB24 at 2.33 A resolution Authors: Joint Center for Structural Genomics (JCSG) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3ez0.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3ez0.ent.gz | 144.6 KB | Display | PDB format |
PDBx/mmJSON format | 3ez0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/3ez0 ftp://data.pdbj.org/pub/pdb/validation_reports/ez/3ez0 | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 25325.436 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arthrobacter sp. FB24 (bacteria) / Gene: YP_832262.1, Arth_2783 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: A0JYP2 #2: Chemical | ChemComp-UNL / Num. of mol.: 4 / Source method: obtained synthetically #3: Chemical | ChemComp-TLA / | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Sequence details | THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH ...THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATI | |
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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: 2.11 Å3/Da / Density % sol: 41.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.47 Details: 20.0% polyethylene glycol 3350, 0.171M potassium sodium tartrate, 0.1M MES pH 6.47, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97918 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 11, 2008 / Details: Flat collimating mirror, toroid focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.33→29.54 Å / Num. obs: 35863 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 5.65 % / Biso Wilson estimate: 46.71 Å2 / Rmerge F obs: 0.191 / Rmerge(I) obs: 0.067 / Rrim(I) all: 0.083 / Net I/σ(I): 10.67 / Num. measured all: 202485 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: SAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.33→29.54 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.75 / SU B: 19.064 / SU ML: 0.227 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.507 / ESU R Free: 0.279 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. L(+)-TARTARIC ACID (TLA) IS PRESENT IN CRYSTALLIZATION CONDITION. 5. UNKNOWN LIGANDS (UNL) WERE MODELED TO ACCOUNT FOR DENSITIES NEAR THE PUTATIVE ACTIVE SITES. THEY RESEMBLE 1-ACYL-GLYCERONE-3-PHOSPHATE. ANOTHER WEAK PEG-LIKE DENSITY NEARBY WAS NOT MODELED.
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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 max: 91.98 Å2 / Biso mean: 46.715 Å2 / Biso min: 22.05 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→29.54 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.33→2.39 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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