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Yorodumi- PDB-3bgu: Crystal structure of a dimeric ferredoxin-like protein of unknown... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3bgu | ||||||
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Title | Crystal structure of a dimeric ferredoxin-like protein of unknown function (tfu_0763) from thermobifida fusca yx at 1.50 A resolution | ||||||
Components | Ferredoxin-like protein of unknown function | ||||||
Keywords | UNKNOWN FUNCTION / Ferredoxin-like fold / stress responsive a/b barrel domain / structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information Stress responsive alpha-beta barrel / Stress responsive A/B Barrel Domain / Stress-response A/B barrel domain profile. / Stress responsive A/B Barrel Domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | Thermobifida fusca (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.5 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of dimeric ferredoxin-like protein of unknown function (YP_288824.1) from Thermobifida fusca YX at 1.50 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bgu.cif.gz | 60.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bgu.ent.gz | 46.9 KB | Display | PDB format |
PDBx/mmJSON format | 3bgu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bgu_validation.pdf.gz | 482.4 KB | Display | wwPDB validaton report |
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Full document | 3bgu_full_validation.pdf.gz | 485.3 KB | Display | |
Data in XML | 3bgu_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3bgu_validation.cif.gz | 18.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bg/3bgu ftp://data.pdbj.org/pub/pdb/validation_reports/bg/3bgu | 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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2 |
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Unit cell |
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Details | SIZE EXCLUSION CHROMATOGRAPHY WITH STATIC LIGHT SCATTERING SUPPORTS THE ASSIGNMENT OF A DIMER AS A SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 13000.149 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Gene: YP_288824.1, Tfu_0763 / Plasmid: speedET / Production host: Escherichia coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q47RW6 |
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-Non-polymers , 5 types, 192 molecules
#2: Chemical | ChemComp-CL / | ||||||
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#3: Chemical | ChemComp-EDO / #4: Chemical | ChemComp-NBZ / | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
-Details
Sequence details | REMARK 999 REMARK 999 SEQUENCE: THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION REMARK 999 TAG ...REMARK 999 REMARK 999 SEQUENCE: 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: 2.22 Å3/Da / Density % sol: 44.63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: NANODROP, 50.0% Ethylene glycol, 5.0% PEG 1000, 0.1M Sodium acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.9537, 0.9798, 0.9797 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 4, 2007 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Double crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→27.206 Å / Num. obs: 35092 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 21.273 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 11.24 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.5→27.206 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.321 / SU ML: 0.064 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.085 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD 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 RECORD CONTAINS RESIDUAL B FACTORS ONLY. 4. RAMACHANDRAN OUTLIER OF RESIDUE ASN-5 AND GLU-6 IN SUBUNIT A IS LOCATED IN POOR DENSITY. 5. N-TERMINAL HIS TAG IN CHAIN A (RESIDUES -3 TO -8) IS SEVERELY DISORDERED. 6. ACETATE AND ETHYLENE GLYCOL ARE MODELED BASED ON CRYSTALLIZATION CONDITIONS. 7. NITROBENZENE (NBZ) WAS MODELED BASED ON ELECTRON DENSITY.
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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: 7.727 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→27.206 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.54 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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