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Yorodumi- PDB-4qus: 1.28 Angstrom resolution crystal structure of predicted acyltrans... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qus | ||||||
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Title | 1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655 | ||||||
Components | Acetyltransferase YpeA | ||||||
Keywords | TRANSFERASE / predicted acyltransferase / acyl-CoA N-acyltransferase domain / GNAT acetyltransferase / CSGID / Structural Genomics / Center for Structural Genomics of Infectious Diseases / NIAID / National Institute of Allergy and Infectious Diseases | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups Similarity search - Function | ||||||
Biological species | Escherichia coli str. K-12 substr. MG1655 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Flores, K.J. / Dubrovska, I. / Shuvalova, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: 1.28 Angstrom resolution crystal structure of predicted acyltransferase with acyl-CoA N-acyltransferase domain (ypeA) from Escherichia coli str. K-12 substr. MG1655 Authors: Halavaty, A.S. / Filippova, E.V. / Minasov, G. / Flores, K.J. / Dubrovska, I. / Shuvalova, L. / 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 | 4qus.cif.gz | 164 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qus.ent.gz | 131.5 KB | Display | PDB format |
PDBx/mmJSON format | 4qus.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qus_validation.pdf.gz | 464.7 KB | Display | wwPDB validaton report |
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Full document | 4qus_full_validation.pdf.gz | 467.7 KB | Display | |
Data in XML | 4qus_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 4qus_validation.cif.gz | 30.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qu/4qus ftp://data.pdbj.org/pub/pdb/validation_reports/qu/4qus | HTTPS FTP |
-Related structure data
Related structure data | 2pdoS 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 17255.553 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli str. K-12 substr. MG1655 (bacteria) Gene: b2434, JW2427, ypeA / Plasmid: pMCSG28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) Magic References: UniProt: P76539, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | #3: Chemical | #4: 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: 2.51 Å3/Da / Density % sol: 51.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 7 mg/mL protein (no tag) in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: the PACT Suite A6 (#6): 0.1 M SPG buffer, pH 9.0, 25% w/v PEG1500, cryo-protection: ...Details: 7 mg/mL protein (no tag) in 10 mM Tris-HCl, pH 8.3, 500 mM sodium chloride, 5 mM BME, crystallization: the PACT Suite A6 (#6): 0.1 M SPG buffer, pH 9.0, 25% w/v PEG1500, cryo-protection: well solution soak, 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-D / Wavelength: 0.9791 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 4, 2014 / Details: Bimorph K-B pair mirrors |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→30 Å / Num. all: 87246 / Num. obs: 87246 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 26.25 |
Reflection shell | Resolution: 1.28→1.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.619 / Mean I/σ(I) obs: 2.5 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2PDO Resolution: 1.28→28.72 Å / Cor.coef. Fo:Fc: 0.986 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.002 / SU ML: 0.02 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.034 / ESU R Free: 0.035 / 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: 20.899 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→28.72 Å
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Refine LS restraints |
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