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Yorodumi- PDB-4j9t: Crystal structure of a putative, de novo designed unnatural amino... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4j9t | ||||||
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Title | Crystal structure of a putative, de novo designed unnatural amino acid dependent metalloprotein, northeast structural genomics consortium target OR61 | ||||||
Components | designed unnatural amino acid dependent metalloprotein | ||||||
Keywords | Structural Genomics / Unknown Function / PSI-Biology / Northeast Structural Genomics Consortium / NESG / a beta-propeller / novel metalloenzyme | ||||||
Function / homology | Function and homology information ganglioside catabolic process / oligosaccharide catabolic process / : / : / : / exo-alpha-sialidase / intracellular membrane-bounded organelle / extracellular region / membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Micromonospora viridifaciens (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Forouhar, F. / Lew, S. / Seetharaman, J. / Mills, J.H. / Khare, S.D. / Everett, J.K. / Baker, D. / Montelione, G.T. / Hunt, J.F. / Tong, L. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Computational design of an unnatural amino Acid dependent metalloprotein with atomic level accuracy. Authors: Mills, J.H. / Khare, S.D. / Bolduc, J.M. / Forouhar, F. / Mulligan, V.K. / Lew, S. / Seetharaman, J. / Tong, L. / Stoddard, B.L. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4j9t.cif.gz | 169.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4j9t.ent.gz | 130.1 KB | Display | PDB format |
PDBx/mmJSON format | 4j9t.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4j9t_validation.pdf.gz | 434.1 KB | Display | wwPDB validaton report |
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Full document | 4j9t_full_validation.pdf.gz | 435 KB | Display | |
Data in XML | 4j9t_validation.xml.gz | 19.3 KB | Display | |
Data in CIF | 4j9t_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/4j9t ftp://data.pdbj.org/pub/pdb/validation_reports/j9/4j9t | HTTPS FTP |
-Related structure data
Related structure data | 4iwwC 4ix0C 1euuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 38549.270 Da / Num. of mol.: 1 Mutation: R68S, I69H, D92A, D131H, F155W, A156E, T226A, F234I, D259S, E260H, R276A, N311D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora viridifaciens (bacteria) Gene: nedA / Plasmid: pET29b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q02834 |
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#2: Chemical | ChemComp-GOL / |
#3: Chemical | ChemComp-ARS / |
#4: Water | ChemComp-HOH / |
Compound details | residue 92, which is modeled as Ala in the current structure, is modified by unnatural amino acid ...residue 92, which is modeled as Ala in the current structure, is modified by unnatural amino acid biprimidine Ala. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2 Å3/Da / Density % sol: 38.45 % |
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Crystal grow | Temperature: 277 K / Method: microbatch under oil / pH: 6.5 Details: protein buffer: 10 mM Tris HCl (pH 8). Precipitation cocktail: 100 MM NA CACODYLATE (PH 6.5), 5 mM FeCl2, 15% PEG 3350 Microbatch under oil, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97012 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 12, 2012 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97012 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→31.021 Å / Num. obs: 61532 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.059 / Rsym value: 0.041 / Net I/σ(I): 29.2 |
Reflection shell | Resolution: 1.4→1.45 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.9 / Num. unique all: 6060 / Rsym value: 0.405 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EUU Resolution: 1.4→31.021 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / σ(I): 1.3 / Phase error: 13.94 / Stereochemistry target values: ML Details: the electron density near Cys-351 was modeled as As ion, however, Fe2+ could be another possibility
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Solvent computation | Shrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.338 Å2 / ksol: 0.396 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.4→31.021 Å
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Refine LS restraints |
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LS refinement shell |
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