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Yorodumi- PDB-4fo1: Crystal structure of lincosamide antibiotic adenylyltransferase L... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4fo1 | |||||||||
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Title | Crystal structure of lincosamide antibiotic adenylyltransferase LnuA, apo | |||||||||
Components | Lincosamide resistance protein | |||||||||
Keywords | TRANSFERASE / STRUCTURAL GENOMICS / ANTIBIOTIC RESISTANCE / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES (CSGID) / NIAID / National Institute of Allergy and Infectious Diseases / ALPHA+BETA STRUCTURE / AMINOGLYCOSIDE-2''-ADENYLYLTRANSFERASE SUPERFAMILY / NUCLEOTIDYLTRANSFERASE SUPERFAMILY / LINCOSAMIDE ADENYLYLTRANSFERASE / LINCOSAMIDE ANTIBIOTICS / LINCOMYCIN / CLINDAMYCIN / ADENOSINE TRIPHOSPHATE / INTRACELLULAR | |||||||||
Function / homology | Aminoglycoside-2''-adenylyltransferase / Aminoglycoside-2''-adenylyltransferase / Beta Polymerase; domain 2 - #40 / Beta Polymerase; domain 2 / Nucleotidyltransferase superfamily / response to antibiotic / 2-Layer Sandwich / Alpha Beta / Lincosamide resistance protein Function and homology information | |||||||||
Biological species | Staphylococcus haemolyticus (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å | |||||||||
Authors | Stogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Kudritska, M. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of lincosamide antibiotic adenylyltransferase LnuA, apo Authors: Stogios, P.J. / Wawrzak, Z. / Minasov, G. / Evdokimova, E. / Egorova, O. / Kudritska, M. / Yim, V. / Courvalin, P. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4fo1.cif.gz | 148.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4fo1.ent.gz | 124.2 KB | Display | PDB format |
PDBx/mmJSON format | 4fo1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4fo1_validation.pdf.gz | 453.5 KB | Display | wwPDB validaton report |
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Full document | 4fo1_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 4fo1_validation.xml.gz | 18 KB | Display | |
Data in CIF | 4fo1_validation.cif.gz | 24.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fo/4fo1 ftp://data.pdbj.org/pub/pdb/validation_reports/fo/4fo1 | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 19253.844 Da / Num. of mol.: 2 / Fragment: LnuA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus haemolyticus (bacteria) / Gene: linA / Plasmid: P15TV LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06107 #2: Chemical | ChemComp-EPE / #3: 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: 2.75 Å3/Da / Density % sol: 55.35 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 1.4 M SODIUM CITRATE, 0.1 M HEPES PH 7.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-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 16, 2011 / Details: MIRRORS |
Radiation | Monochromator: SI-111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97872 Å / Relative weight: 1 |
Reflection | Resolution: 2→29.855 Å / Num. obs: 28239 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -2 / Redundancy: 7.7 % / Rsym value: 0.129 / Net I/σ(I): 15.76 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7.7 % / Mean I/σ(I) obs: 3.75 / Rsym value: 0.569 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.15→29.855 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 27.53 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.15→29.855 Å
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Refine LS restraints |
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LS refinement shell |
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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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