+Open data
-Basic information
Entry | Database: PDB / ID: 2vaq | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF STRICTOSIDINE SYNTHASE IN COMPLEX WITH INHIBITOR | ||||||
Components | STRICTOSIDINE SYNTHASE | ||||||
Keywords | LYASE / ALKALOID METABOLISM / GLYCOPROTEIN / SIX BLADED BETA PROPELLER FOLD / STR1 / SYNTHASE / VACUOLE | ||||||
Function / homology | Function and homology information strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process Similarity search - Function | ||||||
Biological species | RAUVOLFIA SERPENTINA (serpentwood) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Maresh, J. / Giddings, L.A. / Friedrich, A. / Loris, E.A. / Panjikar, S. / Trout, B.L. / Stoeckigt, J. / Peters, B. / O'Connor, S.E. | ||||||
Citation | Journal: J. Am. Chem. Soc. / Year: 2008 Title: Strictosidine synthase: mechanism of a Pictet-Spengler catalyzing enzyme. Authors: Maresh, J.J. / Giddings, L.A. / Friedrich, A. / Loris, E.A. / Panjikar, S. / Trout, B.L. / Stockigt, J. / Peters, B. / O'Connor, S.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2vaq.cif.gz | 133.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2vaq.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 2vaq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/va/2vaq ftp://data.pdbj.org/pub/pdb/validation_reports/va/2vaq | HTTPS FTP |
---|
-Related structure data
Related structure data | 2fp8S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2 / Auth seq-ID: 36 - 331 / Label seq-ID: 14 - 309
NCS oper: (Code: given Matrix: (-0.7584, 0.108, -0.6428), Vector: |
-Components
#1: Protein | Mass: 35765.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: COMPLEX WITH INHIBITOR / Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Variant (production host): M15PREP4 / References: UniProt: P68175, strictosidine synthase #2: Chemical | #3: Water | ChemComp-HOH / | Sequence details | THE SIGNAL PEPTIDE (1-22 RESIDUES) IS NOT INCLUDED IN THE RECOMBINAN | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.76 Å3/Da / Density % sol: 67 % / Description: NONE |
---|---|
Crystal grow | pH: 7 Details: 0.1 MM INHIBITOR, 0.8 M POTASSIUM SODIUM TARTRATE TETRAHYDRATE AND 0.1 M HEPES, PH 7.3 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8148 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 8, 2007 |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8148 Å / Relative weight: 1 |
Reflection | Resolution: 3→20 Å / Num. obs: 20319 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 3→3.05 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.52 / Mean I/σ(I) obs: 3.6 / % possible all: 100 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2FP8 Resolution: 3.01→20 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.905 / SU B: 36.994 / SU ML: 0.311 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.382 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ELECTRON DENSITY FOR THE INHIBITOR BOUND TO B-MOLECULE IS RATHER WEAK. PARTICULARLY INDOLE RING HAS WEAK DENSITY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 48.44 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.01→20 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|