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Yorodumi- PDB-2x0o: Apo structure of the Alcaligin biosynthesis protein C (AlcC) from... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x0o | ||||||
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Title | Apo structure of the Alcaligin biosynthesis protein C (AlcC) from Bordetella bronchiseptica | ||||||
Components | ALCALIGIN BIOSYNTHESIS PROTEIN | ||||||
Keywords | BIOSYNTHETIC PROTEIN / ALCALIGIN BIOSYNTHESIS / ADENYLATION / SIDEROPHORES / IRON ACQUISITION | ||||||
Function / homology | Function and homology information | ||||||
Biological species | BORDETELLA BRONCHISEPTICA (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Johnson, K.A. / Schmelz, S. / Kadi, N. / Mcmahon, S.A. / Oke, M. / Liu, H. / Carter, L.G. / White, M.F. / Challis, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x0o.cif.gz | 242.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x0o.ent.gz | 194.5 KB | Display | PDB format |
PDBx/mmJSON format | 2x0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2x0o_validation.pdf.gz | 441.1 KB | Display | wwPDB validaton report |
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Full document | 2x0o_full_validation.pdf.gz | 445.9 KB | Display | |
Data in XML | 2x0o_validation.xml.gz | 23.3 KB | Display | |
Data in CIF | 2x0o_validation.cif.gz | 32.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x0/2x0o ftp://data.pdbj.org/pub/pdb/validation_reports/x0/2x0o | HTTPS FTP |
-Related structure data
Related structure data | 2ivyC 2jg5C 2jg6C 2vw8C 2vxzC 2wj9C 2x3dC 2x3eC 2x3fC 2x3gC 2x3lC 2x3mC 2x3nC 2x3oC 2x48C 2x4gC 2x4hC 2x4iC 2x4jC 2x4kC 2x4lC 2x5cC 2x5dC 2x5fC 2x5gC 2x5hC 2x5pC 2x5qC 2x5rC 2x5tC 2x7bC 2x7iC 2xu2C 3ffeS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 70047.992 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) BORDETELLA BRONCHISEPTICA (bacteria) / Plasmid: PET-151/TOPO / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P94255 | ||
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#2: Chemical | ChemComp-SO4 / #3: 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: 2.1 Å3/Da / Density % sol: 41 % / Description: NONE |
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Crystal grow | pH: 6 Details: 1.4M MG-SULFATE, 0.1M NA-CACODYLATE, PH6.0, 0.1M LI-SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 1.000005 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.000005 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→40 Å / Num. obs: 23068 / % possible obs: 97.9 % / Observed criterion σ(I): 3.3 / Redundancy: 4.1 % / Biso Wilson estimate: 32 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.1 |
Reflection shell | Resolution: 2.4→2.49 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 3.3 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3FFE Resolution: 2.4→42.901 Å / SU ML: 0.32 / σ(F): 1.99 / Phase error: 22.08 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.938 Å2 / ksol: 0.367 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.1 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→42.901 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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