[English] 日本語
Yorodumi- PDB-1w04: Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex -
+
Open data
-
Basic information
| Entry | Database: PDB / ID: 1w04 | ||||||
|---|---|---|---|---|---|---|---|
| Title | Isopenicillin N Synthase Aminoadipoyl-Cysteinyl-Glycine-Fe-NO Complex | ||||||
Components | ISOPENICILLIN N SYNTHETASE | ||||||
Keywords | OXIDOREDUCTASE / B-LACTAM ANTIBIOTIC / OXYGENASE / PENICILLIN BIOSYNTHESIS | ||||||
| Function / homology | Function and homology informationisopenicillin-N synthase / isopenicillin-N synthase activity / penicillin biosynthetic process / L-ascorbic acid binding / iron ion binding / cytosol Similarity search - Function | ||||||
| Biological species | ![]() | ||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.28 Å | ||||||
Authors | Long, A.J. / Clifton, I.J. / Rutledge, P.J. | ||||||
Citation | Journal: Biochemistry / Year: 2005Title: 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 |
|
-
Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
|---|
-
Downloads & links
-
Download
| PDBx/mmCIF format | 1w04.cif.gz | 91 KB | Display | PDBx/mmCIF format |
|---|---|---|---|---|
| PDB format | pdb1w04.ent.gz | 69.8 KB | Display | PDB format |
| PDBx/mmJSON format | 1w04.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/1w04 ftp://data.pdbj.org/pub/pdb/validation_reports/w0/1w04 | HTTPS FTP |
|---|
-Related structure data
| Related structure data | ![]() 1w03C ![]() 1w05C ![]() 1w06C ![]() 1bk0S S: Starting model for refinement C: citing same article ( |
|---|---|
| Similar structure data |
-
Links
-
Assembly
| Deposited unit | ![]()
| ||||||||
|---|---|---|---|---|---|---|---|---|---|
| 1 |
| ||||||||
| Unit cell |
|
-
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: ![]() |
|---|
-Non-polymers , 5 types, 332 molecules 








| #2: Chemical | ChemComp-HCG / | ||
|---|---|---|---|
| #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 |
|---|
-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
|---|
-
Sample preparation
| Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45 % |
|---|---|
| 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 |
|---|---|
| Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 |
| 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 |
-
Processing
| Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refinement step | Cycle: LAST / Resolution: 1.28→57.74 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| Refine LS restraints |
|
Movie
Controller
About Yorodumi




X-RAY DIFFRACTION
Citation
































PDBj






