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- PDB-3v1s: Scaffold tailoring by a newly detected Pictet-Spenglerase ac-tivi... -

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Basic information

Entry
Database: PDB / ID: 3v1s
TitleScaffold tailoring by a newly detected Pictet-Spenglerase ac-tivity of strictosidine synthase (STR1): from the common tryp-toline skeleton to the rare piperazino-indole framework
ComponentsStrictosidine synthase
KeywordsLYASE / Strictosidine synthase / Alkaloid biosynthesis / Strictosidine synthase family
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-1-yl)ethanamine / Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.328 Å
AuthorsWu, F. / Zhu, H. / Sun, L. / Rajendran, C. / Wang, M. / Ren, X. / Panjikar, S. / Cherkasov, A. / Zou, H. / Stoeckigt, J.
CitationJournal: J.Am.Chem.Soc. / Year: 2012
Title: Scaffold Tailoring by a Newly Detected Pictet-Spenglerase Activity of Strictosidine Synthase: From the Common Tryptoline Skeleton to the Rare Piperazino-indole Framework
Authors: Wu, F. / Zhu, H. / Sun, L. / Rajendran, C. / Wang, M. / Ren, X. / Panjikar, S. / Cherkasov, A. / Zou, H. / Stockigt, J.
History
DepositionDec 10, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 29, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Revision 1.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)71,8524
Polymers71,5322
Non-polymers3202
Water4,540252
1
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9262
Polymers35,7661
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,9262
Polymers35,7661
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)150.976, 150.976, 121.471
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Strictosidine synthase


Mass: 35765.938 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-0LH / 2-(1H-indol-1-yl)ethanamine


Mass: 160.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H12N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.72 Å3/Da / Density % sol: 66.98 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.32→44.5 Å / Num. obs: 44907 / % possible obs: 99.64 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.1_743refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2V91

2v91


Resolution: 2.328→44.496 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8295 / SU ML: 0.71 / σ(F): 2.01 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2296 2204 5 %random
Rwork0.1847 ---
obs0.1869 44082 99.64 %-
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.021 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 162.07 Å2 / Biso mean: 51.6125 Å2 / Biso min: 17.12 Å2
Baniso -1Baniso -2Baniso -3
1--0.2427 Å20 Å20 Å2
2---0.2427 Å2-0 Å2
3---0.4854 Å2
Refinement stepCycle: LAST / Resolution: 2.328→44.496 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4764 0 24 252 5040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084922
X-RAY DIFFRACTIONf_angle_d1.1096692
X-RAY DIFFRACTIONf_chiral_restr0.077718
X-RAY DIFFRACTIONf_plane_restr0.005868
X-RAY DIFFRACTIONf_dihedral_angle_d13.5241756
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3279-2.37850.39961340.36482549268397
2.3785-2.43380.37871380.30832618275699
2.4338-2.49470.32691370.28826052742100
2.4947-2.56210.32521380.269526222760100
2.5621-2.63750.34091380.248826112749100
2.6375-2.72260.29841390.244226382777100
2.7226-2.81990.29971380.223526272765100
2.8199-2.93280.28191370.219126042741100
2.9328-3.06620.25011380.197626252763100
3.0662-3.22790.21391390.178726322771100
3.2279-3.430.25751380.163926222760100
3.43-3.69470.1961380.157926232761100
3.6947-4.06630.19231380.142926262764100
4.0663-4.65420.15161370.121426062743100
4.6542-5.86170.18241390.145526392778100
5.8617-44.50430.18771380.173426312769100
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)
10.8717-0.62660.91511.353-0.60552.46980.0416-0.15430.03410.05750.00710.09530.3593-0.453-0.01570.247-0.10720.00380.330.03370.25769.466935.242610.7797
21.2156-0.4334-0.31531.0777-0.35243.25280.0905-0.0238-0.10860.0794-0.0896-0.12910.70110.31570.00110.32580.0518-0.02810.19790.00380.231926.032631.56852.4114
32.2387-0.5363-0.64471.1166-0.44023.62030.13970.17950.0664-0.0548-0.0619-0.0320.1722-0.0066-0.04030.2180.0151-0.00760.20070.01760.20119.412341.1076-11.2389
42.4817-0.3695-0.89943.2221-0.20492.94360.27590.2672-0.1443-0.2162-0.0492-0.16680.0597-0.4995-0.03370.2317-0.0276-0.03980.3340.01310.22797.634739.9404-2.4644
51.8657-1.1042-0.44220.9578-0.68414.153-0.1242-0.1501-0.14750.3259-0.1025-0.2205-0.4325-0.23610.05810.299-0.0642-0.0430.50680.03230.2855-7.698750.116810.1314
60.60860.3523-0.82552.2949-0.50031.0572-0.0360.4768-0.14110.41210.26760.015-0.0714-0.1959-0.19780.4572-0.0967-0.03480.70340.14790.3646-7.263844.843920.7642
72.0233-1.25860.6252.3947-0.87422.4737-0.5171-0.6409-0.14191.13630.69830.3975-1.1722-0.9734-0.09130.72690.26160.06660.73190.12250.3681-21.112754.220919.4942
82.7893-0.78131.52481.9132-0.82423.6589-0.5183-1.1189-0.58260.94660.87220.3391-0.8616-1.7571-0.11580.73910.33690.16560.96320.25690.5462-31.593555.129816.515
91.6114-0.6004-0.26681.64920.03782.5735-0.1643-0.5719-0.04110.08650.31470.9351-1.0706-1.0385-0.14420.51380.2802-0.02880.80120.12280.4689-30.016858.4717.0855
103.1076-1.2717-0.31042.4154-0.88442.4734-0.3609-0.3033-0.18640.31020.57620.4302-0.7463-1.0825-0.1080.54510.2718-0.09870.72450.07410.3364-28.248860.11561.76
113.47770.21730.3972.6136-0.1913.21550.616-0.0414-0.8472-0.38170.12440.76531.2054-1.4252-0.06350.7936-0.2997-0.4170.6920.10880.606-25.543843.6839-4.1943
122.5582-1.49940.51251.8007-0.39484.05140.2228-0.01660.0328-0.4409-0.1620.03340.0446-0.1141-0.02850.322-0.0312-0.04240.43530.02930.251-15.574951.5746-1.4146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 32:94)A32 - 94
2X-RAY DIFFRACTION2chain 'A' and (resseq 95:228)A95 - 228
3X-RAY DIFFRACTION3chain 'A' and (resseq 229:309)A229 - 309
4X-RAY DIFFRACTION4chain 'A' and (resseq 310:333)A310 - 333
5X-RAY DIFFRACTION5chain 'B' and (resseq 32:67)B32 - 67
6X-RAY DIFFRACTION6chain 'B' and (resseq 68:94)B68 - 94
7X-RAY DIFFRACTION7chain 'B' and (resseq 95:175)B95 - 175
8X-RAY DIFFRACTION8chain 'B' and (resseq 176:203)B176 - 203
9X-RAY DIFFRACTION9chain 'B' and (resseq 204:228)B204 - 228
10X-RAY DIFFRACTION10chain 'B' and (resseq 229:271)B229 - 271
11X-RAY DIFFRACTION11chain 'B' and (resseq 272:287)B272 - 287
12X-RAY DIFFRACTION12chain 'B' and (resseq 288:333)B288 - 333

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