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Yorodumi- PDB-2wpx: Tandem GNAT protein from the clavulanic acid biosynthesis pathway... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2wpx | ||||||
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Title | Tandem GNAT protein from the clavulanic acid biosynthesis pathway (with AcCoA) | ||||||
Components | ORF14 | ||||||
Keywords | TRANSFERASE / ACETYL TRANSFERASE / ANTIBIOTIC BIOSYNTHESIS | ||||||
Function / homology | Function and homology information clavulanic acid biosynthetic process / acyltransferase activity, transferring groups other than amino-acyl groups Similarity search - Function | ||||||
Biological species | STREPTOMYCES CLAVULIGERUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.31 Å | ||||||
Authors | Iqbal, A. / Arunlanantham, H. / McDonough, M.A. / Chowdhury, R. / Clifton, I.J. | ||||||
Citation | Journal: Proteins / Year: 2010 Title: Crystallographic and mass spectrometric analyses of a tandem GNAT protein from the clavulanic acid biosynthesis pathway. Authors: Iqbal, A. / Arunlanantham, H. / Brown, T. / Chowdhury, R. / Clifton, I.J. / Kershaw, N.J. / Hewitson, K.S. / McDonough, M.A. / Schofield, C.J. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2wpx.cif.gz | 152.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2wpx.ent.gz | 121.3 KB | Display | PDB format |
PDBx/mmJSON format | 2wpx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2wpx_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 2wpx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 2wpx_validation.xml.gz | 35.9 KB | Display | |
Data in CIF | 2wpx_validation.cif.gz | 51.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wp/2wpx ftp://data.pdbj.org/pub/pdb/validation_reports/wp/2wpx | HTTPS FTP |
-Related structure data
Related structure data | 2wpwSC 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.021425, -9.9E-5, -0.99977), Vector: |
-Components
#1: Protein | Mass: 36336.707 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) STREPTOMYCES CLAVULIGERUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q8KRB5, 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: 2.79 Å3/Da / Density % sol: 55.97 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 3MG/ML PROTEIN, THREE-FOLD MOLAR EXCESS ACCOA, 1M SODIUM CITRATE, 0.07M CACODYLATE PH6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 |
Detector | Type: ADSC CCD / Detector: CCD / Date: May 31, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.31→32.2 Å / Num. obs: 34742 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 35.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.6 |
Reflection shell | Resolution: 2.31→2.45 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 5.7 / % possible all: 95.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WPW Resolution: 2.31→31.82 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.874 / SU B: 14.298 / SU ML: 0.166 / Cross valid method: THROUGHOUT / ESU R: 0.346 / ESU R Free: 0.253 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.425 Å2
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Refinement step | Cycle: LAST / Resolution: 2.31→31.82 Å
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Refine LS restraints |
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