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Yorodumi- PDB-2x1c: The crystal structure of precursor acyl coenzyme A:isopenicillin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2x1c | ||||||
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Title | The crystal structure of precursor acyl coenzyme A:isopenicillin N acyltransferase from Penicillium chrysogenum | ||||||
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 / MAD / Resolution: 1.85 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 | 2x1c.cif.gz | 292.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2x1c.ent.gz | 248.9 KB | Display | PDB format |
PDBx/mmJSON format | 2x1c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x1/2x1c ftp://data.pdbj.org/pub/pdb/validation_reports/x1/2x1c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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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
#1: Protein | Mass: 39959.172 Da / Num. of mol.: 4 / Mutation: YES 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 #2: Chemical | ChemComp-SO4 / #3: Chemical | ChemComp-GOL / #4: Chemical | #5: Water | ChemComp-HOH / | Compound details | ENGINEERED RESIDUE IN CHAIN A, CYS 103 TO ALA ENGINEERED RESIDUE IN CHAIN B, CYS 103 TO ALA ...ENGINEERED | |
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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: 2.9 Å3/Da / Density % sol: 57.65 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 1.6 M (NH4)2SO4, 0.1 M NACL, 0.1 M HEPES-NAOH, PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.933 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 20, 1999 |
Radiation | Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→48.92 Å / Num. obs: 152842 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 2.93 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 21.51 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 2.72 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.4 / % possible all: 98.6 |
-Processing
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Refinement | Method to determine structure: MAD Starting model: NONE Resolution: 1.85→48.8 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.759 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.105 / 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: 29.853 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→48.8 Å
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Refine LS restraints |
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