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Yorodumi- PDB-4qvt: Crystal structure of predicted N-acyltransferase (ypeA) in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4qvt | ||||||
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Title | Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli | ||||||
Components | Acetyltransferase YpeA | ||||||
Keywords | TRANSFERASE / structural genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / acetyltransferase | ||||||
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 K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.948 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Winsor, G. / Dubrovska, I. / Shuvalova, L. / Wolfe, A.J. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: To be Published Title: Crystal structure of predicted N-acyltransferase (ypeA) in complex with acetyl-CoA from Escherichia coli Authors: Filippova, E.V. / Minasov, G. / Winsor, G. / Dubrovska, I. / Shuvalova, L. / Wolfe, A.J. / 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 | 4qvt.cif.gz | 482.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4qvt.ent.gz | 404.8 KB | Display | PDB format |
PDBx/mmJSON format | 4qvt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4qvt_validation.pdf.gz | 2.7 MB | Display | wwPDB validaton report |
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Full document | 4qvt_full_validation.pdf.gz | 2.7 MB | Display | |
Data in XML | 4qvt_validation.xml.gz | 48.6 KB | Display | |
Data in CIF | 4qvt_validation.cif.gz | 63 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/4qvt ftp://data.pdbj.org/pub/pdb/validation_reports/qv/4qvt | HTTPS FTP |
-Related structure data
Related structure data | 3pdoS 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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-Components
#1: Protein | Mass: 18299.643 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: b2434, JW2427, ypeA / Plasmid: pMCSG28 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 Magic References: UniProt: P76539, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups #2: Chemical | ChemComp-ACO / #3: Chemical | ChemComp-SO4 / #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: 2.25 Å3/Da / Density % sol: 45.27 % |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2 M lithium sulfate, 25% w/v PEG3350, 0.1 M Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 292K |
-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: Jul 4, 2014 / Details: 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: 1.948→69.984 Å / Num. all: 92573 / Num. obs: 92573 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 53.2 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 33.8 |
Reflection shell | Resolution: 1.948→1.98 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.05 / Num. unique all: 4492 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3PDO Resolution: 1.948→69.98 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 10.493 / SU ML: 0.147 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.17 / ESU R Free: 0.156 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.082 Å2
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Refine analyze | Luzzati coordinate error obs: 0.29 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.948→69.98 Å
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Refine LS restraints |
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