[English] 日本語
Yorodumi- PDB-2x7b: Crystal structure of the N-terminal acetylase Ard1 from Sulfolobu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x7b | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the N-terminal acetylase Ard1 from Sulfolobus solfataricus P2 | ||||||
Components | N-ACETYLTRANSFERASE SSO0209 | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information N-terminal methionine Nalpha-acetyltransferase NatE / N-terminal amino-acid Nalpha-acetyltransferase NatA / NatA complex / peptide alpha-N-acetyltransferase activity / metal ion binding Similarity search - Function | ||||||
Biological species | SULFOLOBUS SOLFATARICUS (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Mackay, D. / White, M.F. / Taylor, G.L. / Naismith, J.H. | ||||||
Citation | Journal: J.Struct.Funct.Genomics / Year: 2010 Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs. Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2x7b.cif.gz | 48.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2x7b.ent.gz | 33.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x7b_validation.pdf.gz | 998 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2x7b_full_validation.pdf.gz | 1001.1 KB | Display | |
Data in XML | 2x7b_validation.xml.gz | 9.3 KB | Display | |
Data in CIF | 2x7b_validation.cif.gz | 12 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x7/2x7b ftp://data.pdbj.org/pub/pdb/validation_reports/x7/2x7b | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x0oC 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7iC 2xu2C 2ob0S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 19530.611 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) SULFOLOBUS SOLFATARICUS (archaea) / Strain: P2 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q980R9, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups |
---|---|
#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44 % / Description: NONE |
---|---|
Crystal grow | pH: 5.5 / Details: 25% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.2 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 3, 2008 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→27.84 Å / Num. obs: 11101 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 3.78 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 8.8 / % possible all: 93.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2OB0 Resolution: 1.95→27.84 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.913 / SU B: 4.026 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.206 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FIRST 10 RESIDUES AND THE FINAL RESIDUE ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.479 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→27.84 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|