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- PDB-1w04: Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex -
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Open data
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Basic information
Entry | Database: PDB / ID: 1w04 | ||||||
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Title | Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex | ||||||
![]() | ISOPENICILLIN N SYNTHETASE | ||||||
![]() | OXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS | ||||||
Function / homology | ![]() isopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Long, A.J. / Clifton, I.J. / Rutledge, P.J. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 91 KB | Display | ![]() |
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PDB format | ![]() | 69.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1w03C ![]() 1w05C ![]() 1w06C ![]() 1bk0S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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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.) ![]() ![]() Gene: PCB C / Plasmid: PJB703; OTHER_DETAILS: / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 332 molecules ![](data/chem/img/HCG.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FE2.gif)
![](data/chem/img/HOA.gif)
![](data/chem/img/SO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-HCG / | ||
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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: ![]() |
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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: ![]() ![]() ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 15, 1997 |
Radiation | Monochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.28→16.1 Å / Num. obs: 79915 / % possible obs: 92.6 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 1.28→1.35 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.325 / Mean I/σ(I) obs: 3.2 / % possible all: 85.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BK0 Resolution: 1.28→57.74 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.962 / SU B: 0.625 / SU ML: 0.027 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.046 / 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: 7.23 Å2
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Refinement step | Cycle: LAST / Resolution: 1.28→57.74 Å
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Refine LS restraints |
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