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Yorodumi- PDB-4gpm: Crystal Structure of Engineered Protein. Northeast Structural Gen... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4gpm | ||||||
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Title | Crystal Structure of Engineered Protein. Northeast Structural Genomics Consortium Target OR264. | ||||||
Components | Engineered Protein OR264Engineering | ||||||
Keywords | DE NOVO PROTEIN / Structural Genomics / PSI-Biology / Northeast Structural Genomics Consortium / NESG | ||||||
Function / homology | Ankyrin repeat-containing domain / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha Function and homology information | ||||||
Biological species | synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.002 Å | ||||||
Authors | Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. ...Vorobiev, S. / Su, M. / Parmeggiani, F. / Seetharaman, J. / Huang, P.-S. / Maglaqui, M. / Xiao, R. / Lee, D. / Everett, J.K. / Acton, T.B. / Baker, D. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: NAT.CHEM. / Year: 2017 Title: Computational design of self-assembling cyclic protein homo-oligomers. Authors: Fallas, J.A. / Ueda, G. / Sheffler, W. / Nguyen, V. / McNamara, D.E. / Sankaran, B. / Pereira, J.H. / Parmeggiani, F. / Brunette, T.J. / Cascio, D. / Yeates, T.R. / Zwart, P. / Baker, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4gpm.cif.gz | 127.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4gpm.ent.gz | 100.5 KB | Display | PDB format |
PDBx/mmJSON format | 4gpm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gp/4gpm ftp://data.pdbj.org/pub/pdb/validation_reports/gp/4gpm | HTTPS FTP |
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-Related structure data
Related structure data | 4gmrC 4hb5C 4hxtC 5hryC 5hrzC 5hs0C 5k7vC 5kbaC 5kwdC 2xeeS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
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 | monomer,19.62 kD,98.7% |
-Components
#1: Protein | Mass: 18352.297 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) synthetic construct (others) / Plasmid: pET21, OR264-21.1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic #2: Water | ChemComp-HOH / | |
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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: 1.97 Å3/Da / Density % sol: 37.41 % |
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Crystal grow | Temperature: 291 K / Method: microbatch crystallization under oil / pH: 9 Details: 40% PEG 1000, 0.1M lithium chloride, 0.1M TAPS, pH 9.0 , Microbatch crystallization under oil, temperature 291K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97915 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 9, 2012 |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 1.99→50 Å / Num. all: 37872 / Num. obs: 35751 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 23.73 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 1.99→2.06 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.331 / Mean I/σ(I) obs: 3 / Num. unique all: 3796 / % possible all: 80.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2XEE, chain A Resolution: 2.002→30.139 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.56 / Cross valid method: THROUGHOUT / σ(F): 0.65 / Phase error: 19.8 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.481 Å2 / ksol: 0.401 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 80.64 Å2 / Biso mean: 27.95 Å2 / Biso min: 9.19 Å2
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Refinement step | Cycle: LAST / Resolution: 2.002→30.139 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13
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Refinement TLS params. | S33: 0 Å ° / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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