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- PDB-4iyg: Structure of strictosidine synthase in complex with 2-(1H-INDOL-3... -

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Basic information

Entry
Database: PDB / ID: 4iyg
TitleStructure of strictosidine synthase in complex with 2-(1H-INDOL-3-YL)-N-METHYLETHANAMINE
ComponentsStrictosidine synthase
KeywordsLYASE/LYASE INHIBITOR / strictosidine synthase / LYASE-LYASE INHIBITOR complex
Function / homology
Function and homology information


strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process / endomembrane system / hydrolase activity
Similarity search - Function
Strictosidine synthase, conserved region / Strictosidine synthase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-(1H-indol-3-yl)-N-methylethanamine / Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.702 Å
AuthorsStoeckigt, J. / Fangrui, W. / Wang, M. / Rajendran, C.
CitationJournal: Curr.Med.Chem. / Year: 2015
Title: Using Strictosidine Synthase to Prepare Novel Alkaloids.
Authors: Zhu, H. / Kercmar, P. / Wu, F. / Rajendran, C. / Sun, L. / Wang, M. / Stockigt, J.
History
DepositionJan 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 1.3Feb 24, 2016Group: Database references
Revision 1.4Aug 3, 2016Group: Data collection

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Strictosidine synthase
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,5613
Polymers67,3872
Non-polymers1741
Water2,108117
1
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,8682
Polymers33,6941
Non-polymers1741
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Strictosidine synthase


Theoretical massNumber of molelcules
Total (without water)33,6941
Polymers33,6941
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.230, 150.230, 122.101
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Strictosidine synthase


Mass: 33693.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: STR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P68175, EC: 4.3.3.2
#2: Chemical ChemComp-1HU / 2-(1H-indol-3-yl)-N-methylethanamine


Mass: 174.242 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H14N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 117 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.93 Å3/Da / Density % sol: 68.74 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→38.296 Å / Num. obs: 27655 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.702→38.296 Å / SU ML: 0.44 / σ(F): 2.01 / σ(I): 2 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 1382 5 %5%
Rwork0.2117 ---
all0.2137 ---
obs0.2137 27655 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.702→38.296 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4759 0 13 117 4889
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094905
X-RAY DIFFRACTIONf_angle_d1.3076669
X-RAY DIFFRACTIONf_dihedral_angle_d16.0941753
X-RAY DIFFRACTIONf_chiral_restr0.086716
X-RAY DIFFRACTIONf_plane_restr0.005867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.702-2.79860.39671310.33292496X-RAY DIFFRACTION94
2.7986-2.91060.34891400.30652662X-RAY DIFFRACTION99
2.9106-3.0430.36521390.29032643X-RAY DIFFRACTION99
3.043-3.20330.32771410.26012672X-RAY DIFFRACTION99
3.2033-3.40390.28241390.23112648X-RAY DIFFRACTION99
3.4039-3.66650.24371390.2062639X-RAY DIFFRACTION99
3.6665-4.03520.23391390.18982647X-RAY DIFFRACTION99
4.0352-4.61820.20461400.15942647X-RAY DIFFRACTION99
4.6182-5.81520.20041370.16892614X-RAY DIFFRACTION98
5.8152-38.30010.20181370.18892605X-RAY DIFFRACTION97

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