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Yorodumi- PDB-3fse: Crystal structure of a two-domain protein containing dj-1/thij/pf... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3fse | ||||||
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Title | Crystal structure of a two-domain protein containing dj-1/thij/pfpi-like and ferritin-like domains (ava_4496) from anabaena variabilis atcc 29413 at 1.90 A resolution | ||||||
Components | two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains | ||||||
Keywords | HYDROLASE / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Ferritin, core subunit, four-helix bundle / Ferritin / Class I glutamine amidotransferase-like / Ferritin-like / Ferritin-like superfamily ...Deglycase PfpI / PfpI endopeptidase domain profile. / DJ-1/PfpI / DJ-1/PfpI family / Class I glutamine amidotransferase (GATase) domain / Ferritin, core subunit, four-helix bundle / Ferritin / Class I glutamine amidotransferase-like / Ferritin-like / Ferritin-like superfamily / Up-down Bundle / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Anabaena variabilis ATCC 29413 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of two-domain protein containing DJ-1/ThiJ/PfpI-like and ferritin-like domains. (YP_324989.1) from ANABAENA VARIABILIS ATCC 29413 at 1.90 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 | 3fse.cif.gz | 149.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fse.ent.gz | 120.9 KB | Display | PDB format |
PDBx/mmJSON format | 3fse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3fse_validation.pdf.gz | 449.7 KB | Display | wwPDB validaton report |
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Full document | 3fse_full_validation.pdf.gz | 458.1 KB | Display | |
Data in XML | 3fse_validation.xml.gz | 30.2 KB | Display | |
Data in CIF | 3fse_validation.cif.gz | 45 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/3fse ftp://data.pdbj.org/pub/pdb/validation_reports/fs/3fse | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | AUTHORS STATE THAT ANALYTICAL SIZE EXCLUSION CHROMATOGRAPHY AND CRYSTAL PACKING ANALYSIS SUPPORT THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE IN SOLUTION |
-Components
#1: Protein | Mass: 40327.117 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anabaena variabilis ATCC 29413 (bacteria) Gene: Ava_4496, YP_324989.1 / Plasmid: SpeedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q3M4J2 #2: Chemical | ChemComp-EDO / | #3: 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: 2.08 Å3/Da / Density % sol: 40.79 % Description: THE AND R MERGE VALUES STATISTICS REPORTED HERE ARE BASED ON TREATING FRIEDEL PAIRS AS SEPARATE REFLECTIONS Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.67 | Details: 20.0% polyethylene glycol 6000, 0.15M magnesium acetate, 0.1M sodium cacodylate pH 6.67, NANODROP', VAPOR DIFFUSION, SITTING DROP, temperature 277K |
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97953 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 11, 2008 / Details: Adjustable focusing mirrors in K-B geometry | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97953 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→29.975 Å / Num. obs: 52666 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 29.913 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 8.92 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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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: 1.9→29.975 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.15 / SU B: 6.944 / SU ML: 0.103 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.158 / ESU R Free: 0.144 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. ATOM RECORDS CONTAIN 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 RECORDS CONTAIN 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 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 4. RESIDUE CYS 111 SEEMS PARTIALLY OXIDIZED AND COULD BE FUNCTIONALLY RELEVANT.
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 79.59 Å2 / Biso mean: 43.403 Å2 / Biso min: 21.56 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→29.975 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 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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