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Yorodumi- PDB-2c43: STRUCTURE OF AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE- PHOSPHOPANT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2c43 | ||||||
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Title | STRUCTURE OF AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE- PHOSPHOPANTETHEINYL TRANSFERASE IN COMPLEX WITH COENZYME A | ||||||
Components | AMINOADIPATE-SEMIALDEHYDE DEHYDROGENASE-PHOSPHOPANTETHEINYL TRANSFERASE | ||||||
Keywords | TRANSFERASE / FATTY ACID BIOSYNTHESIS / COENZYME A | ||||||
Function / homology | Function and homology information pantothenate metabolic process / 10-formyltetrahydrofolate catabolic process / holo-[acyl-carrier-protein] synthase / Vitamin B5 (pantothenate) metabolism / lysine biosynthetic process via aminoadipic acid / holo-[acyl-carrier-protein] synthase activity / protein maturation / magnesium ion binding / extracellular exosome / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.93 Å | ||||||
Authors | Bunkoczi, G. / Wu, X. / Dubinina, E. / Johansson, C. / Smee, C. / Turnbull, A. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. ...Bunkoczi, G. / Wu, X. / Dubinina, E. / Johansson, C. / Smee, C. / Turnbull, A. / von Delft, F. / Arrowsmith, C. / Edwards, A. / Sundstrom, M. / Weigelt, J. / Oppermann, U. | ||||||
Citation | Journal: Chem. Biol. / Year: 2007 Title: Mechanism and substrate recognition of human holo ACP synthase. Authors: Bunkoczi, G. / Pasta, S. / Joshi, A. / Wu, X. / Kavanagh, K.L. / Smith, S. / Oppermann, U. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2c43.cif.gz | 79.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2c43.ent.gz | 56.8 KB | Display | PDB format |
PDBx/mmJSON format | 2c43.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2c43_validation.pdf.gz | 715.4 KB | Display | wwPDB validaton report |
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Full document | 2c43_full_validation.pdf.gz | 717.1 KB | Display | |
Data in XML | 2c43_validation.xml.gz | 14.5 KB | Display | |
Data in CIF | 2c43_validation.cif.gz | 20.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c4/2c43 ftp://data.pdbj.org/pub/pdb/validation_reports/c4/2c43 | HTTPS FTP |
-Related structure data
Related structure data | 2bydSC 2cg5C 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: 37438.309 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PCOEX-1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: Q9P0Q3, UniProt: Q9NRN7*PLUS, L-aminoadipate-semialdehyde dehydrogenase |
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#2: Chemical | ChemComp-COA / |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-CL / |
#5: 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: 42 % |
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Crystal grow | Details: 10% PEG6K 2.0 M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Aug 29, 2005 |
Radiation | Monochromator: OSMIC HR MULTILAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→32.79 Å / Num. obs: 19791 / % possible obs: 80.3 % / Observed criterion σ(I): 0 / Redundancy: 5.04 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 16.53 |
Reflection shell | Resolution: 1.93→2.02 Å / Redundancy: 0.69 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.59 / % possible all: 29.2 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 2BYD Resolution: 1.93→49.39 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.349 / SU ML: 0.112 / TLS residual ADP flag: UNVERIFIED / Cross valid method: THROUGHOUT / ESU R: 0.18 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.63 Å2
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Refinement step | Cycle: LAST / Resolution: 1.93→49.39 Å
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Refine LS restraints |
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