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- PDB-4imb: Structure of strictosidine synthase in complex with 2-(1-methyl-1... -

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Basic information

Entry
Database: PDB / ID: 4imb
TitleStructure of strictosidine synthase in complex with 2-(1-methyl-1H-indol-3-yl)ethanamine
ComponentsStrictosidine synthase
KeywordsLYASE/LYASE INHIBITOR / Strictosidine synthase / strictosidine / 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-(1-methyl-1H-indol-3-yl)ethanamine / Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.703 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 2, 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: Database references
Revision 1.5Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water63135
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)149.782, 149.782, 121.789
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-1ES / 2-(1-methyl-1H-indol-3-yl)ethanamine


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.: 35 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.9 Å3/Da / Density % sol: 68.47 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 5, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→37.445 Å / Num. all: 27472 / Num. obs: 27432 / Observed criterion σ(I): 2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8_1069) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.703→37.445 Å / SU ML: 0.43 / σ(F): 2 / Phase error: 31.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2726 1371 5 %0.2726
Rwork0.2082 ---
all0.2726 27432 --
obs0.2115 27427 98.34 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.703→37.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 13 35 4751
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094847
X-RAY DIFFRACTIONf_angle_d1.3226599
X-RAY DIFFRACTIONf_dihedral_angle_d16.0621714
X-RAY DIFFRACTIONf_chiral_restr0.088714
X-RAY DIFFRACTIONf_plane_restr0.006860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7028-2.79930.41981370.3432594X-RAY DIFFRACTION98
2.7993-2.91140.38521370.32072615X-RAY DIFFRACTION99
2.9114-3.04380.38531370.30662615X-RAY DIFFRACTION99
3.0438-3.20420.33961380.27852617X-RAY DIFFRACTION99
3.2042-3.40490.29381380.23412634X-RAY DIFFRACTION99
3.4049-3.66750.25771380.19492609X-RAY DIFFRACTION99
3.6675-4.03620.25551370.1762611X-RAY DIFFRACTION99
4.0362-4.61940.22511370.14882607X-RAY DIFFRACTION99
4.6194-5.81640.22321370.16272593X-RAY DIFFRACTION98
5.8164-37.44910.22121350.18022561X-RAY DIFFRACTION96
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0775-0.1663-0.05910.17790.05310.2230.1132-0.63290.044-0.1453-0.0889-0.6463-0.0444-0.56720.00050.5652-0.1197-0.01330.52160.07860.47867.016634.97186.5395
21.1108-0.1310.65520.3017-0.31891.79430.1730.07310.01180.0236-0.0273-0.07990.15080.085800.52520.029-0.02120.3284-0.01380.483822.578434.8347-0.6787
30.1601-0.1350.01170.0728-0.01970.10980.18970.29920.08210.6936-0.2829-0.602-0.3237-0.4270.00080.5736-0.0172-0.10540.48210.00670.45758.211539.5625-1.5091
40.0946-0.06680.13530.013-0.07820.15250.39320.13540.12950.0923-0.4887-0.0270.2298-0.1663-00.4866-0.1412-0.10220.609-0.00850.4541-8.104549.13938.1223
50.1489-0.16930.00930.15930.03980.11840.0923-0.00110.00030.0450.2993-0.21640.4138-0.43340.00040.6327-0.0504-0.06640.8810.03060.593-5.562749.647215.4047
60.26660.09810.08570.06350.01190.2498-0.269-0.438-0.24680.05530.08490.1363-0.4122-0.67110.00010.8979-0.0234-0.0470.870.11090.6986-14.187147.835620.6918
70.0364-0.03750.00710.0281-0.0084-0.0205-0.50190.0561-0.14390.15380.15080.3319-0.13240.1641-0.00091.16960.1147-0.08551.04630.04670.7579-16.118954.182824.9133
80.2306-0.15410.06120.15720.06730.0557-0.1886-0.0756-0.42070.69050.2911-0.0425-0.5735-0.4897-0.00021.01480.2370.15090.91340.13180.8393-26.83754.883117.556
90.2337-0.08340.03240.0679-0.0980.1206-0.8062-0.4443-0.77060.45250.82560.0453-0.3816-0.4613-0.00051.14350.07670.11120.95770.10891.2831-31.492354.605916.8187
100.257-0.13160.13730.09680.0580.129-0.1169-0.0188-0.372-0.07340.09731.0655-0.6481-0.0741-0.00110.86840.1005-0.07770.8690.02410.8731-31.461860.86456.694
110.1362-0.08810.21180.0547-0.12230.16030.1156-0.3457-0.14040.22890.3521-0.09610.0159-0.70460.00030.6718-0.0622-0.18130.85360.07550.6712-24.958956.769-0.1923
120.2419-0.00480.11880.0629-0.01660.30580.4556-0.0136-0.0355-0.3621-0.2257-0.030.2535-0.34010.00260.853-0.12-0.23280.75290.01850.6063-22.518647.8755-4.5121
130.2179-0.06340.05460.05990.01920.15690.04730.1248-0.0944-0.2255-0.247-0.25080.09770.0783-0.00040.5633-0.1089-0.0540.69330.04430.6128-11.423650.41192.1262
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 32 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 309 )
3X-RAY DIFFRACTION3chain 'A' and (resid 310 through 332 )
4X-RAY DIFFRACTION4chain 'B' and (resid 33 through 52 )
5X-RAY DIFFRACTION5chain 'B' and (resid 53 through 82 )
6X-RAY DIFFRACTION6chain 'B' and (resid 83 through 120 )
7X-RAY DIFFRACTION7chain 'B' and (resid 121 through 139 )
8X-RAY DIFFRACTION8chain 'B' and (resid 140 through 175 )
9X-RAY DIFFRACTION9chain 'B' and (resid 176 through 203 )
10X-RAY DIFFRACTION10chain 'B' and (resid 204 through 243 )
11X-RAY DIFFRACTION11chain 'B' and (resid 244 through 271 )
12X-RAY DIFFRACTION12chain 'B' and (resid 272 through 309 )
13X-RAY DIFFRACTION13chain 'B' and (resid 310 through 333 )

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