+Open data
-Basic information
Entry | Database: PDB / ID: 3nfd | ||||||
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Title | Chronobacterium ammoniagenes ACPS-CoA complex | ||||||
Components | Phosphopantetheine protein transferase, Ppt1p | ||||||
Keywords | TRANSFERASE / acyl carrier protein synthase / Mycobacterium tuberculosis / acyl carrier protein / fatty acid synthase | ||||||
Function / homology | Function and homology information holo-[acyl-carrier-protein] synthase / holo-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Corynebacterium ammoniagenes (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å | ||||||
Authors | Gokulan, K. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2011 Title: Mycobacterium tuberculosis acyl carrier protein synthase adopts two different pH-dependent structural conformations. Authors: Gokulan, K. / Aggarwal, A. / Shipman, L. / Besra, G.S. / Sacchettini, J.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3nfd.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3nfd.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 3nfd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3nfd_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 3nfd_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 3nfd_validation.xml.gz | 39.6 KB | Display | |
Data in CIF | 3nfd_validation.cif.gz | 51.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nf/3nfd ftp://data.pdbj.org/pub/pdb/validation_reports/nf/3nfd | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 16956.828 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Corynebacterium ammoniagenes (bacteria) Gene: PPT1 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: O31302 #2: Chemical | ChemComp-COA / #3: Water | ChemComp-HOH / | Sequence details | ACCORDING TO THE AUTHORS THE DISCREPANC | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.42 % |
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Crystal grow | Method: evaporation / pH: 6.5 Details: 25% PEG MME 5K, 0.1 M MES, 200 mM ammonium sulfate, pH 6.5, EVAPORATION |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 1-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 10, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.89→30.52 Å / Num. all: 52264 / Num. obs: 52264 / % possible obs: 73 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 58.1 |
Reflection shell | Resolution: 1.89→1.95 Å / Redundancy: 0.8 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 6.4 / % possible all: 44.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→20 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.906 / SU B: 3.329 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.211 / 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: 24.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.89→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.89→1.936 Å / Total num. of bins used: 20 /
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