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Yorodumi- PDB-2a4n: Crystal structure of aminoglycoside 6'-N-acetyltransferase comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2a4n | ||||||
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Title | Crystal structure of aminoglycoside 6'-N-acetyltransferase complexed with coenzyme A | ||||||
Components | aac(6')-Ii | ||||||
Keywords | TRANSFERASE / alpha beta protein / N-acetyl transferase | ||||||
Function / homology | Function and homology information acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | Enterococcus faecium (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Burk, D.L. / Xiong, B. / Breitbach, C. / Berghuis, A.M. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Structures of aminoglycoside acetyltransferase AAC(6')-Ii in a novel crystal form: structural and normal-mode analyses. Authors: Burk, D.L. / Xiong, B. / Breitbach, C. / Berghuis, A.M. #1: Journal: Protein Sci. / Year: 2003 Title: Crystal Structure Of Aminoglycoside 6'-Acetyltransferase Type II In Complex With Coenzyme A Authors: Burk, D.L. / Ghuman, N. / Wybenga-Groot, L.E. / Berghuis, A.M. #2: Journal: Structure / Year: 1999 Title: Crystal structure of an aminoglycoside 6'-N-acetyltransferase: defining the GCN5-related N-acetyltransferase superfamily fold Authors: Wybenga-Groot, L.E. / Draker, K. / Wright, G.D. / Berghuis, A.M. | ||||||
History |
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Remark 999 | SEQUENCE THE AUTHOR STATES THAT THERE IS AN ERROR IN THE SEQUENCE DATABASE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2a4n.cif.gz | 94.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2a4n.ent.gz | 70.7 KB | Display | PDB format |
PDBx/mmJSON format | 2a4n.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2a4n_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 2a4n_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 2a4n_validation.xml.gz | 18.6 KB | Display | |
Data in CIF | 2a4n_validation.cif.gz | 25.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a4/2a4n ftp://data.pdbj.org/pub/pdb/validation_reports/a4/2a4n | HTTPS FTP |
-Related structure data
Related structure data | 1n71S S: Starting model for refinement |
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Similar structure data |
-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 on special symmetry positions |
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Details | The asymmetric unit contains the biological unit (dimer). |
-Components
#1: Protein | Mass: 20730.195 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterococcus faecium (bacteria) / Gene: aac(6')-Ii / Plasmid: pPLaac-1 / Species (production host): Escherichia coli Production host: Escherichia coli str. K12 substr. W3110 (bacteria) Strain (production host): W3110 References: UniProt: Q47764, aminoglycoside 6'-N-acetyltransferase #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: 2.114 Å3/Da / Density % sol: 40 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: HEPES, EDTA, coenzyme A, 2-(6'-N-sisomycin)acetic acid, tri-sodium citrate, ammonium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X8C / Wavelength: 1.072 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 6, 2002 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.072 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→100 Å / Num. all: 18341 / Num. obs: 18341 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.019 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible obs: 91.2 % / Rmerge(I) obs: 0.233 / Num. measured obs: 1663 / Χ2: 0.553 / % possible all: 95.4 |
-Phasing
Phasing MR | Method rotation: fast direct / Method translation: &STRIP%trans_method |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1N71 Resolution: 2.2→48.43 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 365371.719 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 55.169 Å2 / ksol: 0.35 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 28 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→48.43 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: RESTRAINTS | |||||||||||||||||||||||||
LS refinement shell | Resolution: 2.2→2.34 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
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Xplor file |
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