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Yorodumi- PDB-3hyk: 2.31 Angstrom resolution crystal structure of a holo-(acyl-carrie... -
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-Basic information
Entry | Database: PDB / ID: 3hyk | ||||||
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Title | 2.31 Angstrom resolution crystal structure of a holo-(acyl-carrier-protein) synthase from Bacillus anthracis str. Ames in complex with CoA (3',5'-ADP) | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / Holo-(Acyl-Carrier-Protein) Synthase / Structural Genomics / Infectious Diseases / Center for Structural Genomics of Infectious Diseases / Fatty acid biosynthesis / Lipid synthesis / Magnesium / Metal-binding / CSGID | ||||||
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 | Bacillus anthracis (anthrax bacterium) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Skarina, T. / Onopriyenko, O. / Papazisi, L. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2012 Title: Structural characterization and comparison of three acyl-carrier-protein synthases from pathogenic bacteria. Authors: Halavaty, A.S. / Kim, Y. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Kwon, K. / Peterson, S.N. / Joachimiak, A. / ...Authors: Halavaty, A.S. / Kim, Y. / Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Zhou, M. / Onopriyenko, O. / Skarina, T. / Papazisi, L. / Kwon, K. / Peterson, S.N. / Joachimiak, A. / Savchenko, A. / Anderson, W.F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hyk.cif.gz | 99.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hyk.ent.gz | 76.2 KB | Display | PDB format |
PDBx/mmJSON format | 3hyk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3hyk_validation.pdf.gz | 2.3 MB | Display | wwPDB validaton report |
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Full document | 3hyk_full_validation.pdf.gz | 2.3 MB | Display | |
Data in XML | 3hyk_validation.xml.gz | 21.7 KB | Display | |
Data in CIF | 3hyk_validation.cif.gz | 29.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hy/3hyk ftp://data.pdbj.org/pub/pdb/validation_reports/hy/3hyk | HTTPS FTP |
-Related structure data
Related structure data | 3qmnC 4jm7C 3f09 C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | |
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: 13533.095 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Bacillus anthracis str. Ames / Gene: acpS, BA_0250, GBAA_0250, BAS0236 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3) References: UniProt: Q81JG3, holo-[acyl-carrier-protein] synthase #2: Chemical | ChemComp-MG / #3: Chemical | ChemComp-CL / #4: Chemical | ChemComp-A3P / #5: Water | ChemComp-HOH / | |
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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: 2.63 Å3/Da / Density % sol: 53.19 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: protein was mixed at 1:1 v/v ratio with PEG3350 25%, 0.2M MgCl2, 0.1M Hepes pH 7.5, 10mM CoA. 5% Glycerol, 5% sucrose, 55 Eth. Gl. in magic sol., paratone were used as cryo protectants. , ...Details: protein was mixed at 1:1 v/v ratio with PEG3350 25%, 0.2M MgCl2, 0.1M Hepes pH 7.5, 10mM CoA. 5% Glycerol, 5% sucrose, 55 Eth. Gl. in magic sol., paratone were used as cryo protectants. , VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 4, 2009 / Details: beryllium lenses |
Radiation | Monochromator: single diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→34.99 Å / Num. all: 19381 / Num. obs: 19381 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 30.2 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 20.54 |
Reflection shell | Resolution: 2.31→2.35 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.553 / Mean I/σ(I) obs: 4.9 / Num. unique all: 969 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3F09 3f09 Resolution: 2.31→34.99 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 12.325 / SU ML: 0.166 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.35 / ESU R Free: 0.245 / 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: 16.961 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→34.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.307→2.367 Å / Total num. of bins used: 20
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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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