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Yorodumi- PDB-3kxw: The crystal structure of fatty acid AMP ligase from Legionella pn... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3kxw | ||||||
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Title | The crystal structure of fatty acid AMP ligase from Legionella pneumophila | ||||||
Components | Saframycin Mx1 synthetase B | ||||||
Keywords | LIGASE / Fatty acid AMP ligase / SGX / acyl adenylate / Structural Genomics / PSI-2 / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC | ||||||
Function / homology | Function and homology information adenylyltransferase activity / fatty acid biosynthetic process / plasma membrane Similarity search - Function | ||||||
Biological species | Legionella pneumophila subsp. pneumophila (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.851 Å | ||||||
Authors | Zhang, Z. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2011 Title: Structural and Functional Studies of Fatty Acyl Adenylate Ligases from E. coli and L. pneumophila. Authors: Zhang, Z. / Zhou, R. / Sauder, J.M. / Tonge, P.J. / Burley, S.K. / Swaminathan, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kxw.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kxw.ent.gz | 111.5 KB | Display | PDB format |
PDBx/mmJSON format | 3kxw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kxw_validation.pdf.gz | 651.9 KB | Display | wwPDB validaton report |
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Full document | 3kxw_full_validation.pdf.gz | 659.9 KB | Display | |
Data in XML | 3kxw_validation.xml.gz | 28.7 KB | Display | |
Data in CIF | 3kxw_validation.cif.gz | 44.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kx/3kxw ftp://data.pdbj.org/pub/pdb/validation_reports/kx/3kxw | HTTPS FTP |
-Related 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: 67864.523 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Legionella pneumophila subsp. pneumophila (bacteria) Strain: strain Philadelphia 1 / ATCC 33152 / DSM 7513 / Gene: lpg2229 / Plasmid: BC - pSGX3 (BC) / Production host: Escherichia coli (E. coli) Strain (production host): BL21 (DE3) - Codon + RIL - Stratagene References: UniProt: Q5ZTD3 |
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#2: Chemical | ChemComp-1ZZ / |
#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: 2.64 Å3/Da / Density % sol: 53.43 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 25% PEG 3350 and 0.2 M NaCl, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9792 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 16, 2009 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9792 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→31 Å / Num. obs: 54877 / % possible obs: 89.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.5 % / Biso Wilson estimate: 19.25 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 10.9 |
Reflection shell | Resolution: 1.85→1.9 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 4 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 1.851→31 Å / SU ML: 0.24 / Isotropic thermal model: Isotropic / Stereochemistry target values: Engh & Huber
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 44.979 Å2 / ksol: 0.391 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 19.25 Å2
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Refinement step | Cycle: LAST / Resolution: 1.851→31 Å
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Refine LS restraints |
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LS refinement shell |
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