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Yorodumi- PDB-1w06: Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe NO Complex -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w06 | ||||||
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Title | Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Alanine-Fe NO Complex | ||||||
Components | ISOPENICILLIN N SYNTHETASE | ||||||
Keywords | OXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS | ||||||
Function / homology | Function and homology information isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | Emericella nidulans (mold) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Long, A.J. / Clifton, I.J. / Rutledge, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2005 Title: Structural Studies on the Reaction of Isopenicillin N Synthase with the Truncated Substrate Analogues Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-Glycine and Delta-(L-Alpha-Aminoadipoyl)-L-Cysteinyl-D- Alanine Authors: Long, A.J. / Clifton, I.J. / Roach, P.L. / Baldwin, J.E. / Schofield, C.J. / Rutledge, P.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w06.cif.gz | 89.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w06.ent.gz | 67.2 KB | Display | PDB format |
PDBx/mmJSON format | 1w06.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w06_validation.pdf.gz | 705.8 KB | Display | wwPDB validaton report |
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Full document | 1w06_full_validation.pdf.gz | 709 KB | Display | |
Data in XML | 1w06_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 1w06_validation.cif.gz | 27.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/1w06 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/1w06 | HTTPS FTP |
-Related structure data
Related structure data | 1w03C 1w04C 1w05C 1bk0S 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: 37563.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Emericella nidulans (strain FGSC A4 / ATCC 38163 / CBS 112.46 / NRRL 194 / M139) (mold) Gene: PCB C / Plasmid: PJB703; OTHER_DETAILS: / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): NM554 / References: UniProt: P05326, isopenicillin-N synthase |
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-Non-polymers , 5 types, 345 molecules
#2: Chemical | ChemComp-W05 / | ||
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#3: Chemical | ChemComp-FE2 / | ||
#4: Chemical | ChemComp-HOA / | ||
#5: Chemical | #6: Water | ChemComp-HOH / | |
-Details
Compound details | CATALYTIC ACTIVITY: N-[(5S)-5-AMINO-5-CARBOXYPEN |
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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: 2.26 Å3/Da / Density % sol: 45 % |
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Crystal grow | pH: 8.5 Details: 1.0M LITHIUM SULPHATE, 76MM TRIS/HCL (PH8.5), pH 8.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.997 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.997 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→22 Å / Num. obs: 38692 / % possible obs: 92.3 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.115 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.409 / % possible all: 85 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK0 Resolution: 1.65→58.72 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.95 / SU B: 2.758 / SU ML: 0.094 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.102 / ESU R Free: 0.1 / 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: 10.42 Å2
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Refinement step | Cycle: LAST / Resolution: 1.65→58.72 Å
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Refine LS restraints |
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