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Yorodumi- PDB-2q0z: Crystal structure of Q9P172/Sec63 from Homo sapiens. Northeast St... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2q0z | ||||||
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Title | Crystal structure of Q9P172/Sec63 from Homo sapiens. Northeast Structural Genomics Target HR1979. | ||||||
Components | Protein PRO2281 | ||||||
Keywords | PROTEIN TRANSPORT / sec63 / sec / NESG / hr1979 / structural genomics / translocase / Northeast Structural Genomics Consortium / PSI-2 / Protein Structure Initiative | ||||||
Function / homology | Function and homology information cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity ...cis assembly of pre-catalytic spliceosome / spliceosome conformational change to release U4 (or U4atac) and U1 (or U11) / U2-type catalytic step 1 spliceosome / U2-type precatalytic spliceosome / mRNA Splicing - Minor Pathway / U5 snRNP / U4/U6 x U5 tri-snRNP complex / catalytic step 2 spliceosome / mRNA Splicing - Major Pathway / helicase activity / spliceosomal complex / mRNA splicing, via spliceosome / osteoblast differentiation / RNA helicase activity / RNA helicase / ATP hydrolysis activity / RNA binding / nucleoplasm / ATP binding / membrane / identical protein binding / nucleus Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2 Å | ||||||
Authors | Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. ...Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG) | ||||||
Citation | Journal: To be Published Title: Crystal structure of Q9P172/Sec63 from Homo sapiens. Authors: Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / ...Authors: Benach, J. / Neely, H. / Abashidze, M. / Edstrom, W.C. / Seetharaman, J. / Zhao, L. / Fang, Y. / Cunningham, K. / Owens, L. / Ma, L.-C. / Xiao, R. / Liu, J. / Baran, M.C. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2q0z.cif.gz | 76.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2q0z.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 2q0z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/2q0z ftp://data.pdbj.org/pub/pdb/validation_reports/q0/2q0z | 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 39092.496 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: Liver / Plasmid: pET14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+Magic / References: UniProt: Q9P172, UniProt: O75643*PLUS |
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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: 2.45 Å3/Da / Density % sol: 49.7 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6 Details: 0.2M K/Na tartrate, 0.1M Sodium citrate pH 5.6, 1M Ammonium sulfate, 0.5M Imidazole pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9793 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: May 8, 2007 / Details: mirrors | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Redundancy: 11.3 % / Av σ(I) over netI: 8.2 / Number: 662162 / Rmerge(I) obs: 0.102 / Χ2: 0.69 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 58497 / % possible obs: 99.9 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 1.9→50 Å / Num. obs: 58497 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 11.3 % / Rmerge(I) obs: 0.102 / Χ2: 0.69 / Net I/σ(I): 8.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing dm | FOM : 0.71 / FOM acentric: 0.72 / FOM centric: 0.65 / Reflection: 28346 / Reflection acentric: 25916 / Reflection centric: 2430 | |||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2→20 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING
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Solvent computation | Bsol: 50.839 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.823 Å2
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Refinement step | Cycle: LAST / Resolution: 2→20 Å
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Refine LS restraints |
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Xplor file |
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