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- PDB-6n5v: Crystal Structure of Strictosidine in complex with 1H-indole-4-et... -

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Basic information

Entry
Database: PDB / ID: 6n5v
TitleCrystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine
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 / indole alkaloid metabolic process / alkaloid biosynthetic process / vacuole / endomembrane system
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-4-yl)ethan-1-amine / Strictosidine synthase 1
Similarity search - Component
Biological speciesRauvolfia serpentina (serpentwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.549 Å
AuthorsCai, Y. / Shao, N. / Xie, H. / Futamura, Y. / Panjikar, S. / Liu, H. / Zhu, H. / Osada, H. / Zou, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21472170 China
Citation
Journal: to be published
Title: Crystal Structure of Strictosidine in complex with 1H-indole-4-ethanamine
Authors: Cai, Y. / Shao, N. / Xie, H. / Futamura, Y. / Panjikar, S. / Liu, H. / Zhu, H. / Osada, H. / Zou, H.
#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. / Stoeckigt, J.
History
DepositionNov 22, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 23, 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)70,7354
Polymers70,4152
Non-polymers3202
Water1629
1
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3682
Polymers35,2071
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,3682
Polymers35,2071
Non-polymers1601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)150.400, 150.400, 122.610
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: 35207.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rauvolfia serpentina (serpentwood) / Gene: STR1 / Plasmid: PQE-2 / Production host: Escherichia coli (E. coli) / Strain (production host): M15PREP4 / References: UniProt: P68175, EC: 4.3.3.2
#2: Chemical ChemComp-KDY / 2-(1H-indol-4-yl)ethan-1-amine


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


Mass: 18.015 Da / Num. of mol.: 9 / 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: 3.58 Å3/Da / Density % sol: 68.8 % / Description: Hexagonal
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 7.5
Details: 0.8 M potassium sodium tartrate tetrahydrate and 0.1 M HEPES, pH 7.4, 5 mg/mL strictosidine synthase, 3 mM 4-IEA (1H-indole-4-ethanamine)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jul 1, 2017 / Details: DCM
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.549→37.6 Å / Num. obs: 64264 / % possible obs: 95.2 % / Redundancy: 2.23 % / Biso Wilson estimate: 65 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.064 / Net I/σ(I): 9.3
Reflection shellResolution: 2.55→2.7 Å / Redundancy: 2.27 % / Rmerge(I) obs: 0.71 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 10128 / CC1/2: 0.906 / Rrim(I) all: 0.839 / % possible all: 93.4

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSVERSION Jan 26, 2018 BUILT=20180126data reduction
XDSVERSION Jan 26, 2018 BUILT=20180126data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V91

2v91


Resolution: 2.549→37.6 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 33.89
RfactorNum. reflection% reflectionSelection details
Rfree0.2472 989 3.08 %993
Rwork0.207 ---
obs0.2083 32132 95.29 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 81 Å2
Refinement stepCycle: LAST / Resolution: 2.549→37.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4810 0 24 9 4843
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014970
X-RAY DIFFRACTIONf_angle_d1.1636762
X-RAY DIFFRACTIONf_dihedral_angle_d7.0072906
X-RAY DIFFRACTIONf_chiral_restr0.078728
X-RAY DIFFRACTIONf_plane_restr0.008876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5493-2.68370.45891330.3954393X-RAY DIFFRACTION94
2.6837-2.85180.30751380.3124548X-RAY DIFFRACTION97
2.8518-3.07190.33511620.28914540X-RAY DIFFRACTION98
3.0719-3.38080.30261300.25474532X-RAY DIFFRACTION97
3.3808-3.86960.2511290.22484367X-RAY DIFFRACTION93
3.8696-4.87360.21741380.16614429X-RAY DIFFRACTION95
4.8736-37.60410.20041590.15944334X-RAY DIFFRACTION93

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