+Open data
-Basic information
Entry | Database: PDB / ID: 1sjw | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of polyketide cyclase SnoaL | ||||||
Components | nogalonic acid methyl ester cyclase | ||||||
Keywords | LYASE / Anthracyclines / Nogalamycin / SnoaL / aldol condensation / Structural Genomics / Structural Proteomics in Europe / SPINE | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Streptomyces nogalater (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.35 Å | ||||||
Authors | Sultana, A. / Kallio, P. / Jansson, A. / Wang, J.S. / Neimi, J. / Mantsala, P. / Schneider, G. / Structural Proteomics in Europe (SPINE) | ||||||
Citation | Journal: Embo J. / Year: 2004 Title: Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation. Authors: Sultana, A. / Kallio, P. / Jansson, A. / Wang, J.S. / Niemi, J. / Schneider, G. #1: Journal: To be Published Title: Crystallization and preliminary crystallographic data of SnoaL, a polyketide cyclase in nogalamycin biosynthesis Authors: Sultana, A. / Kallio, P. / Jansson, A. / Neimi, J. / Mantsala, P. / Schneider, G. | ||||||
History |
| ||||||
Remark 999 | SEQUENCE THE AUTHORS STATE THAT THE SNOAL GENE STARTS EARLIER THAN PREDICTED FROM THE ORIGINALLY ...SEQUENCE THE AUTHORS STATE THAT THE SNOAL GENE STARTS EARLIER THAN PREDICTED FROM THE ORIGINALLY DEPOSITED SEQUENCE. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1sjw.cif.gz | 80.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1sjw.ent.gz | 59.7 KB | Display | PDB format |
PDBx/mmJSON format | 1sjw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1sjw_validation.pdf.gz | 738.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1sjw_full_validation.pdf.gz | 744.4 KB | Display | |
Data in XML | 1sjw_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | 1sjw_validation.cif.gz | 8.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sj/1sjw ftp://data.pdbj.org/pub/pdb/validation_reports/sj/1sjw | HTTPS FTP |
-Related structure data
Similar structure data | |
---|---|
Other databases |
-Links
-Assembly
Deposited unit |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| |||||||||||||||
2 |
| |||||||||||||||
Unit cell |
| |||||||||||||||
Components on special symmetry positions |
| |||||||||||||||
Details | The biological assembly is a tetramer generated from the one monomer in the assymetric unit by the operations (-1,-1,0),(-1,0,-1),(0,-1,-1). |
-Components
#1: Protein | Mass: 16788.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces nogalater (bacteria) / Gene: SnoaL / Plasmid: pBAD/hisB / Production host: Escherichia coli (E. coli) / Strain (production host): Top10 / References: UniProt: Q9RN59 |
---|---|
#2: Chemical | ChemComp-NGV / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 42.74 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PEG4000, Tris HCl, Na Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction |
| |||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source |
| |||||||||||||||
Detector |
| |||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
| |||||||||||||||
Reflection | Resolution: 1.35→36.03 Å / Num. obs: 35447 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.3 % / Biso Wilson estimate: 16.57 Å2 / Rsym value: 0.085 / Net I/σ(I): 23.3 | |||||||||||||||
Reflection shell | Resolution: 1.35→1.42 Å / Redundancy: 8.3 % / Mean I/σ(I) obs: 3.4 / Rsym value: 0.485 / % possible all: 98.5 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: SIRAS Starting model: Built by ARP/WARP Resolution: 1.35→36.03 Å / Num. parameters: 12538 / Num. restraintsaints: 15347 / Isotropic thermal model: Anisotropic / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY SHELX
| |||||||||||||||||||||||||
Displacement parameters |
| |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1101 / Occupancy sum non hydrogen: 1347.25 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.35→36.03 Å
| |||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||
LS refinement shell | Resolution: 1.35→36.03 Å
|