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- PDB-6s5m: Strictosidine Synthase from Ophiorrhiza pumila in complex with (S... -

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Basic information

Entry
Database: PDB / ID: 6s5m
TitleStrictosidine Synthase from Ophiorrhiza pumila in complex with (S)-1-n-propyl-2,3,4,9-tetrahydro-1H-beta-carboline
ComponentsStrictosidine synthase
KeywordsLYASE / alkaloid / C-C bond / Pictet-Spenglerase
Function / homology
Function and homology information


vacuole / endomembrane system / hydrolase activity
Similarity search - Function
Strictosidine synthase-like, N-terminal / 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-KWH / Strictosidine synthase
Similarity search - Component
Biological speciesOphiorrhiza pumila (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsEger, E. / Sharma, M. / Kroutil, W. / Grogan, G.
CitationJournal: J.Am.Chem.Soc. / Year: 2020
Title: Inverted Binding of Non-natural Substrates in Strictosidine Synthase Leads to a Switch of Stereochemical Outcome in Enzyme-Catalyzed Pictet-Spengler Reactions.
Authors: Eger, E. / Simon, A. / Sharma, M. / Yang, S. / Breukelaar, W.B. / Grogan, G. / Houk, K.N. / Kroutil, W.
History
DepositionJul 2, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 1.2Nov 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

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Assembly

Deposited unit
A: Strictosidine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9842
Polymers36,7701
Non-polymers2141
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.365, 78.756, 62.213
Angle α, β, γ (deg.)90.000, 93.220, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Strictosidine synthase


Mass: 36769.902 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ophiorrhiza pumila (plant) / Gene: str / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle / References: UniProt: Q94LW9
#2: Chemical ChemComp-KWH / (1~{S})-1-propyl-2,3,4,9-tetrahydro-1~{H}-pyrido[3,4-b]indole


Mass: 214.306 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H18N2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.1 M Tris-HCL pH 8.0, 0.3 M NH4Cl, 20% PEG 6K

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 19, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 1.9→54.84 Å / Num. obs: 28720 / % possible obs: 98.9 % / Redundancy: 4.1 % / CC1/2: 1 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.04 / Net I/σ(I): 7.5
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 1858 / CC1/2: 0.95 / Rpim(I) all: 0.44 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2FP9

2fp9


Resolution: 1.9→54.84 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.953 / SU B: 6.417 / SU ML: 0.165 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2433 1472 5.1 %RANDOM
Rwork0.2033 ---
obs0.2054 27248 98.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 100.67 Å2 / Biso mean: 48.876 Å2 / Biso min: 33.24 Å2
Baniso -1Baniso -2Baniso -3
1-3.61 Å2-0 Å2-5.69 Å2
2---0.45 Å2-0 Å2
3----2.5 Å2
Refinement stepCycle: final / Resolution: 1.9→54.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2359 0 16 74 2449
Biso mean--69.84 55.45 -
Num. residues----306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0132442
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172150
X-RAY DIFFRACTIONr_angle_refined_deg1.5711.6473323
X-RAY DIFFRACTIONr_angle_other_deg1.3281.5894974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0155305
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.50422.927123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.34915356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8751511
X-RAY DIFFRACTIONr_chiral_restr0.080.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022795
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02547
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 113 -
Rwork0.354 2018 -
all-2131 -
obs--99.53 %

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