+Open data
-Basic information
Entry | Database: PDB / ID: 2pge | ||||||
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Title | Crystal structure of MenC from Desulfotalea psychrophila LSv54 | ||||||
Components | MenC | ||||||
Keywords | LYASE / MenC / OSBS / 9393a / NYSGXRC / PSI-II / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Desulfotalea psychrophila LSv54 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å | ||||||
Authors | Agarwal, R. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2014 Title: Loss of quaternary structure is associated with rapid sequence divergence in the OSBS family. Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. ...Authors: Odokonyero, D. / Sakai, A. / Patskovsky, Y. / Malashkevich, V.N. / Fedorov, A.A. / Bonanno, J.B. / Fedorov, E.V. / Toro, R. / Agarwal, R. / Wang, C. / Ozerova, N.D. / Yew, W.S. / Sauder, J.M. / Swaminathan, S. / Burley, S.K. / Almo, S.C. / Glasner, M.E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pge.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pge.ent.gz | 64.5 KB | Display | PDB format |
PDBx/mmJSON format | 2pge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pge ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pge | HTTPS FTP |
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-Related structure data
Related structure data | 1wueC 1wufC 2oktC 2olaC 2oztC 3cawC 3h70C 3h7vC 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: 41690.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Desulfotalea psychrophila LSv54 (bacteria) Species: Desulfotalea psychrophila / Strain: LSv54, DSM 12343 / Gene: MenC, DP0251 / Plasmid: pSGX3(BC) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)codon+RIL References: UniProt: Q6ARP5, Lyases; Carbon-oxygen lyases; Hydro-lyases |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.2 % |
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Crystal grow | Temperature: 278 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 0.1M MES, 12% PEG 20000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 278K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2007 / Details: mirrors |
Radiation | Monochromator: SI-III / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→50 Å / Num. all: 57812 / Num. obs: 57812 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Redundancy: 13.1 % / Biso Wilson estimate: 18 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.6→1.66 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2 / Num. unique all: 4828 / % possible all: 83.5 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.6→35.7 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 88860.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The missing residues listed in Remark 465 are due to lack of or weak electron density in those regions.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 33.0102 Å2 / ksol: 0.353215 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 20.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→35.7 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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