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Yorodumi- PDB-6cy6: Crystal structure of spermidine/spermine N-acetyltransferase SpeG... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6cy6 | ||||||
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Title | Crystal structure of spermidine/spermine N-acetyltransferase SpeG from Escherichia coli in complex with tris(hydroxymethyl)aminomethane. | ||||||
Components | Spermidine N(1)-acetyltransferase | ||||||
Keywords | TRANSFERASE / SpeG / spermidine / GNAT / N-acetyltransferase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information diamine N-acetyltransferase complex / spermidine catabolic process / spermine catabolic process / diamine N-acetyltransferase / diamine N-acetyltransferase activity / polyamine catabolic process / coenzyme A metabolic process / magnesium ion binding / protein-containing complex / identical protein binding Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å | ||||||
Authors | Filippova, E.V. / Minasov, G. / Kiryukhina, O. / Anderson, W.F. / Satchell, K.J.F. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2019 Title: Analysis of crystalline and solution states of ligand-free spermidine N-acetyltransferase (SpeG) from Escherichia coli. Authors: Filippova, E.V. / Weigand, S. / Kiryukhina, O. / 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 | 6cy6.cif.gz | 94.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6cy6.ent.gz | 70.5 KB | Display | PDB format |
PDBx/mmJSON format | 6cy6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6cy6_validation.pdf.gz | 464.9 KB | Display | wwPDB validaton report |
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Full document | 6cy6_full_validation.pdf.gz | 465 KB | Display | |
Data in XML | 6cy6_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 6cy6_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cy/6cy6 ftp://data.pdbj.org/pub/pdb/validation_reports/cy/6cy6 | HTTPS FTP |
-Related structure data
Related structure data | 4r9mSC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 21920.035 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Strain: K12 / Gene: speG, b1584, JW1576 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) magic / References: UniProt: P0A951, diamine N-acetyltransferase |
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-Non-polymers , 6 types, 121 molecules
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-NA / | #4: Chemical | ChemComp-TRS / | #5: Chemical | #6: Chemical | ChemComp-MPD / ( #7: 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: 2.47 Å3/Da / Density % sol: 50.28 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.2 M Ammonium phosphate monobasic, 0.1 M Tris, 50% v/v MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2016 / Details: Beryllium Lenses |
Radiation | Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30 Å / Num. obs: 22903 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.048 / Rmerge(I) obs: 0.048 / Net I/σ(I): 51.1 |
Reflection shell | Resolution: 1.75→1.78 Å / Redundancy: 13 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 4.3 / Num. unique obs: 1109 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4R9M Resolution: 1.75→93.1 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.952 / SU B: 3.547 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.091 / ESU R Free: 0.099 / 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: 31.44 Å2
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Refinement step | Cycle: 1 / Resolution: 1.75→93.1 Å
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