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- PDB-2v91: STRUCTURE OF STRICTOSIDINE SYNTHASE IN COMPLEX WITH STRICTOSIDINE -

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Basic information

Entry
Database: PDB / ID: 2v91
TitleSTRUCTURE OF STRICTOSIDINE SYNTHASE IN COMPLEX WITH STRICTOSIDINE
ComponentsSTRICTOSIDINE SYNTHASE
KeywordsLYASE / ALKALOID METABOLISM / SIX BLADED BETA PROPELLER FOLD / STR1 / VACUOLE / SYNTHASE / GLYCOPROTEIN
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
Chem-S55 / Strictosidine synthase
Similarity search - Component
Biological speciesRAUVOLFIA SERPENTINA (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.01 Å
AuthorsLoris, E.A. / Panjikar, S. / Ruppert, M. / Barleben, L. / Unger, M. / Stoeckigt, J.
Citation
Journal: Chem.Biol. / Year: 2007
Title: Structure Based Engineering of Strictosidine Synthase: Auxiliary for Alkaloid Libraries
Authors: Loris, E.A. / Panjikar, S. / Ruppert, M. / Barleben, L. / Unger, M. / Schubel, H. / Stoeckigt, J.
#1: Journal: Plant Cell / Year: 2006
Title: The Structure of Rauvolfia Serpentina Strictosidine Synthase is a Novel Six-Bladed Beta- Propeller Fold in Plant Proteins
Authors: Ma, X. / Panjikar, S. / Koepke, J. / Loris, E. / Stockigt, J.
History
DepositionAug 16, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)68,4524
Polymers67,3872
Non-polymers1,0652
Water99155
1
A: STRICTOSIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2262
Polymers33,6941
Non-polymers5331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: STRICTOSIDINE SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2262
Polymers33,6941
Non-polymers5331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)150.177, 150.177, 121.707
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEULEULEUAA35 - 3314 - 300
21LEULEULEULEUBB35 - 3314 - 300
12S55S55S55S55AC1334
22S55S55S55S55BD1334

NCS ensembles :
ID
1
2

NCS oper: (Code: given
Matrix: (-0.7666, 0.1005, -0.6342), (-0.04837, -0.9939, -0.09901), (-0.6403, -0.04523, 0.7668)
Vector: 62.43, 133.5, 31.51)

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Components

#1: Protein STRICTOSIDINE SYNTHASE


Mass: 33693.602 Da / Num. of mol.: 2 / Fragment: RESIDUES 32-333
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH STRICTOSIDINE / Source: (gene. exp.) RAUVOLFIA SERPENTINA (serpentwood) / Plasmid: PQE-2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15PREP4 / References: UniProt: P68175, EC: 4.3.3.2
#2: Chemical ChemComp-S55 / METHYL (2S,3R,4S)-3-ETHYL-2-(BETA-D-GLUCOPYRANOSYLOXY)-4-[(1S)-2,3,4,9-TETRAHYDRO-1H-BETA-CARBOLIN-1-YLMETHYL]-3,4-DIHYDRO-2H-PYRAN-5-CARBOXYLATE


Mass: 532.583 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H36N2O9
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsFIRST 28 RESIDUES ARE EXCLUDED IN CLONING

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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: 3.58 Å3/Da / Density % sol: 65.68 % / Description: NONE
Crystal growpH: 7.5
Details: 0.8M POTASSIUM SODIUM TARTRATE TETRAHYDRATE, 100MM HEPES-NA, 1MM TRYPTAMINE, PH 7.5,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8076
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 28, 2005 / Details: DOUBLE CRYSTAL SI 111
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8076 Å / Relative weight: 1
ReflectionResolution: 3.01→20 Å / Num. obs: 20423 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.8 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 21.2
Reflection shellResolution: 3→3.05 Å / Redundancy: 11.7 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2FP8

2fp8


Resolution: 3.01→20 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.914 / SU B: 14.209 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.359 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.235 959 4.7 %RANDOM
Rwork0.192 ---
obs0.194 19336 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.14 Å2
Baniso -1Baniso -2Baniso -3
1-5.39 Å22.7 Å20 Å2
2--5.39 Å20 Å2
3----8.09 Å2
Refinement stepCycle: LAST / Resolution: 3.01→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4727 0 76 55 4858
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214943
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8411.9626746
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4025602
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.130.2735
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023834
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2410.22359
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2207
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.222
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5050.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5791.52993
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.182.54846
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.96551950
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.619101900
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A1188tight positional0.080.05
12B1188tight positional0.080.05
11A1133medium positional0.390.5
12B1133medium positional0.390.5
21A38medium positional0.170.5
22B38medium positional0.170.5
11A1188tight thermal0.51.5
12B1188tight thermal0.51.5
11A1133medium thermal1.42.5
12B1133medium thermal1.42.5
21A38medium thermal2.572.5
22B38medium thermal2.572.5
LS refinement shellResolution: 3.01→3.08 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.353 73
Rwork0.276 1407
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)
11.9560.2508-0.5861.06310.36464.6099-0.01110.03970.0603-0.02870.06060.1237-0.155-0.3847-0.04950.00890.0252-0.00820.09350.03080.173120.911652.3030.0285
25.22120.7757-2.33441.33910.29984.4155-0.0363-0.42310.5384-0.03120.1055-0.1335-0.1110.4551-0.06920.20860.01820.00030.10470.02610.337955.917577.96210.2172
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 333
2X-RAY DIFFRACTION2B32 - 333

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