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Yorodumi- PDB-3e49: Crystal structure of a prokaryotic domain of unknown function (du... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3.0E+49 | ||||||
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Title | Crystal structure of a prokaryotic domain of unknown function (duf849) with a tim barrel fold (bxe_c0966) from burkholderia xenovorans lb400 at 1.75 A resolution | ||||||
Components | uncharacterized protein DUF849 with a TIM barrel fold | ||||||
Keywords | METAL BINDING PROTEIN / Structural genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI-2 | ||||||
Function / homology | Function and homology information L-lysine catabolic process to acetate / transferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | Burkholderia xenovorans LB400 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å | ||||||
Authors | Joint Center for Structural Genomics (JCSG) | ||||||
Citation | Journal: To be published Title: Crystal structure of prokaryotic domain of unknown function (DUF849) with a TIM barrel fold (YP_556190.1) from BURKHOLDERIA XENOVORANS LB400 at 1.75 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 | 3e49.cif.gz | 265.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3e49.ent.gz | 218.5 KB | Display | PDB format |
PDBx/mmJSON format | 3e49.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e4/3e49 ftp://data.pdbj.org/pub/pdb/validation_reports/e4/3e49 | 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: Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: SER / End label comp-ID: PHE / Refine code: 6 / Auth seq-ID: 4 - 310 / Label seq-ID: 5 - 311
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Details | AUTHORS STATE THAT THE CRYSTAL PACKING ANALYSIS SUGGESTS THE ASSIGNMENT OF A TETRAMER AS THE SIGNIFICANT OLIGOMERIZATION STATE. |
-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 34407.680 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans LB400 (bacteria) Gene: YP_556190.1, Bxeno_C0912, Bxe_C0966 / Plasmid: SpeedET / Production host: Escherichia Coli (E. coli) / Strain (production host): HK100 / References: UniProt: Q13GE9 |
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-Non-polymers , 5 types, 964 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-ETX / #4: Chemical | #5: Chemical | ChemComp-IMD / #6: Water | ChemComp-HOH / | |
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-Details
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: 2.22 Å3/Da / Density % sol: 44.55 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 40.0000% 2-ethoxyethanol, 0.0500M Ca(OAc)2, 0.1M Imidazole pH 8.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837,0.97936,0.97892 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jul 17, 2008 / 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: 1.75→29.656 Å / Num. obs: 115967 / % possible obs: 97.2 % / Redundancy: 2.7 % / Biso Wilson estimate: 21.904 Å2 / Rmerge(I) obs: 0.069 / Rsym value: 0.069 / Net I/σ(I): 6.6 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 1.75→29.656 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.503 / SU ML: 0.106 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.121 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. X-RAY FLUORESCENCE EXCITATION AND WAVELENGTH SCANS AND ANOMALOUS DIFFERENCE FOURIERS SUPPORT THE MODELING OF ZN IONS. 4. ACT, ETX, AND IMD MOLECULES FROM THE CRYSTALLIZATION SOLUTION ARE MODELED. 5. RAMACHANDRAN OUTLIER RESIDUE C95 IS IN A POORLY DEFINED REGION.
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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 mean: 24.44 Å2
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Refinement step | Cycle: LAST / Resolution: 1.75→29.656 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 3751 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 1.75→1.795 Å / Total num. of bins used: 20
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