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Yorodumi- PDB-2x1e: The crystal structure of mature acyl coenzyme A:isopenicillin N a... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x1e | ||||||
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Title | The crystal structure of mature acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum in complex 6- aminopenicillanic acid | ||||||
Components | ACYL-COENZYME | ||||||
Keywords | TRANSFERASE / ZYMOGEN / NTN-HYDROLASE / PENICILLIN BIOSYNTHESIS / ACYLTRANSFERASE / ANTIBIOTIC BIOSYNTHESIS | ||||||
Function / homology | Function and homology information isopenicillin-N N-acyltransferase / isopenicillin-N N-acyltransferase activity / acyl coenzyme A: isopenicillin N acyltransferase activity / penicillin biosynthetic process / peroxisomal matrix Similarity search - Function | ||||||
Biological species | PENICILLIUM CHRYSOGENUM (fungus) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Bokhove, M. / Yoshida, H. / Hensgens, C.M.H. / van der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W. | ||||||
Citation | Journal: Structure / Year: 2010 Title: Structures of an Isopenicillin N Converting Ntn-Hydrolase Reveal Different Catalytic Roles for the Active Site Residues of Precursor and Mature Enzyme. Authors: Bokhove, M. / Yoshida, H. / Hensgens, C.M.H. / Van Der Laan, J.M. / Sutherland, J.D. / Dijkstra, B.W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2x1e.cif.gz | 287.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x1e.ent.gz | 234.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x1e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/2x1e ftp://data.pdbj.org/pub/pdb/validation_reports/x1/2x1e | HTTPS FTP |
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-Related structure data
Related structure data | 2x1cC 2x1dSC C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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4 |
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Unit cell |
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 40023.234 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PENICILLIUM CHRYSOGENUM (fungus) / Strain: AS-P-78 / Plasmid: PKC787 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 References: UniProt: P15802, isopenicillin-N N-acyltransferase |
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-Non-polymers , 5 types, 407 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-X1E / ( | #5: Chemical | ChemComp-CL / | #6: 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: 50.17 % / Description: NONE |
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Crystal grow | pH: 6.9 / Details: pH 6.9 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.976 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 25, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.61 Å / Num. obs: 102192 / % possible obs: 98.9 % / Observed criterion σ(I): 0 / Redundancy: 3.77 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.29 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 3.75 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 3.8 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2X1D Resolution: 2→33.63 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.944 / SU B: 8.026 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.174 / ESU R Free: 0.143 / 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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.359 Å2
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Refinement step | Cycle: LAST / Resolution: 2→33.63 Å
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Refine LS restraints |
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