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Yorodumi- PDB-5cxd: 1.75 Angstrom resolution crystal structure of the apo-form acyl-c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5cxd | ||||||
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Title | 1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group | ||||||
Components | Holo-[acyl-carrier-protein] synthase | ||||||
Keywords | TRANSFERASE / acyl-carrier-protein synthase / AcpS / FAS II / structural genomics / CSGID / Center for Structural Genomics of Infectious Diseases | ||||||
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 | Staphylococcus aureus (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Halavaty, A.S. / Minasov, G. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To Be Published Title: 1.75 Angstrom resolution crystal structure of the apo-form acyl-carrier-protein synthase (AcpS) (acpS; purification tag off) from Staphylococcus aureus subsp. aureus COL in the I4 space group Authors: Halavaty, A.S. / Minasov, G. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) #1: Journal: Acta Crystallogr. D Biol. Crystallogr. / 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 | 5cxd.cif.gz | 175.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5cxd.ent.gz | 138.9 KB | Display | PDB format |
PDBx/mmJSON format | 5cxd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5cxd_validation.pdf.gz | 459 KB | Display | wwPDB validaton report |
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Full document | 5cxd_full_validation.pdf.gz | 461.9 KB | Display | |
Data in XML | 5cxd_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 5cxd_validation.cif.gz | 28.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cx/5cxd ftp://data.pdbj.org/pub/pdb/validation_reports/cx/5cxd | HTTPS FTP |
-Related structure data
Related structure data | 4jm7S S: Starting model for refinement |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Refine code: _
NCS ensembles :
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-Components
#1: Protein | Mass: 13899.824 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (strain COL) (bacteria) Strain: COL / Gene: acpS, SACOL2061 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic References: UniProt: Q5HED0, holo-[acyl-carrier-protein] synthase #2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-PEG / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.27 Å3/Da / Density % sol: 45.79 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: Protein (purification tag off): 4.6 mg/mL in 10 mM Tris-HCL pH 8.3, 500 mM NaCl 5 mM BME 1 mM CaCl2 150 mM imidazole Crystallization: The PACT Suite B8(20): 200 mM Ammonium chloride 100 mM ...Details: Protein (purification tag off): 4.6 mg/mL in 10 mM Tris-HCL pH 8.3, 500 mM NaCl 5 mM BME 1 mM CaCl2 150 mM imidazole Crystallization: The PACT Suite B8(20): 200 mM Ammonium chloride 100 mM MES pH 6.0 20 % (w/v) PEG 6000 Cryo: crystallization condition |
-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 29, 2015 |
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: 1.75→30 Å / Num. all: 37637 / Num. obs: 37637 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 24.3 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 22.86 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 2.34 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4JM7 Resolution: 1.75→29.29 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.528 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.113 / 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: 29.084 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→29.29 Å
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Refine LS restraints |
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