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- PDB-2fpb: Structure of Strictosidine Synthase, the Biosynthetic Entry to th... -

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Basic information

Entry
Database: PDB / ID: 2fpb
TitleStructure of Strictosidine Synthase, the Biosynthetic Entry to the Monoterpenoid Indole Alkaloid Family
ComponentsStrictosidine Synthase
KeywordsLYASE / six bladed beta propeller fold / STR1 / Synthase
Function / homology
Function and homology information


strictosidine synthase / strictosidine synthase activity / alkaloid metabolic process / vacuole / biosynthetic process
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)ETHANAMINE / Strictosidine synthase
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsPanjikar, S.
CitationJournal: 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
DepositionJan 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 23, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_source ...database_2 / diffrn_source / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)72,5594
Polymers72,2392
Non-polymers3202
Water3,117173
1
A: Strictosidine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2802
Polymers36,1191
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strictosidine Synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2802
Polymers36,1191
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)148.936, 148.936, 121.344
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

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg label comp-ID: LEU / End label comp-ID: VAL / Refine code: 2 / Auth seq-ID: 35 - 332 / Label seq-ID: 13 - 310

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Strictosidine Synthase /


Mass: 36119.457 Da / Num. of mol.: 2 / Mutation: I65M,L116M,I190M,L203M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Plasmid: pQE-2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15[pREP4] / References: UniProt: P68175, strictosidine synthase
#2: Chemical ChemComp-TSS / 2-(1H-INDOL-3-YL)ETHANAMINE / TRYPTAMINE / Tryptamine


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


Mass: 18.015 Da / Num. of mol.: 173 / Source method: isolated from a natural source / Formula: H2O

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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 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 7.5
Details: 0.8M potassium sodium tartrate tetrahydrate, 100mM HEPES-Na, 1mM Tryptamine, pH 7.5, VAPOR DIFFUSION, temperature 295.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9714 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 14, 2004 / Details: double crystal Si[111]
RadiationMonochromator: SILICON 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9714 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 24731 / Num. obs: 23380 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 44 Å2 / Rmerge(I) obs: 0.099 / Net I/σ(I): 3
Reflection shellResolution: 2.8→2.84 Å / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MAR345data collection
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.906 / SU B: 12.402 / SU ML: 0.233 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.57 / ESU R Free: 0.286 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.21717 1253 5.1 %RANDOM
Rwork0.16363 ---
all0.17 ---
obs0.16631 23380 99.9 %-
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: 23.105 Å2
Baniso -1Baniso -2Baniso -3
1-4.54 Å22.27 Å20 Å2
2--4.54 Å20 Å2
3----6.81 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 24 173 5007
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0214971
X-RAY DIFFRACTIONr_angle_refined_deg1.7071.956755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1525608
X-RAY DIFFRACTIONr_chiral_restr0.1130.2720
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023844
X-RAY DIFFRACTIONr_nbd_refined0.2340.22184
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2201
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2960.230
X-RAY DIFFRACTIONr_mcbond_it0.6761.53029
X-RAY DIFFRACTIONr_mcangle_it1.3322.54901
X-RAY DIFFRACTIONr_scbond_it3.3351942
X-RAY DIFFRACTIONr_scangle_it5.054101854
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1192tight positional0.080.05
1152medium positional0.450.5
1192tight thermal0.511.5
1152medium thermal1.352.5
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 85
Rwork0.294 1748
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)
10.79540.2674-0.32261.80550.58264.4093-0.00330.0547-0.09710.08660.1216-0.10050.30180.3081-0.11820.11140.12-0.03580.1301-0.02420.2327109.2230.698-0.24
20.9319-0.6113-0.91143.48381.68184.39510.1080.02320.1786-0.422-0.0086-0.279-0.6641-0.0367-0.09950.26290.0023-0.0010.1563-0.02490.3215113.50644.122-11.009
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA35 - 33213 - 310
2X-RAY DIFFRACTION2BB35 - 33213 - 310

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