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- PDB-5fi3: HETEROYOHIMBINE SYNTHASE THAS1 FROM CATHARANTHUS ROSEUS - COMPLEX... -

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Basic information

Entry
Database: PDB / ID: 5fi3
TitleHETEROYOHIMBINE SYNTHASE THAS1 FROM CATHARANTHUS ROSEUS - COMPLEX WITH NADP+
ComponentsTetrahydroalstonine synthase
KeywordsOXIDOREDUCTASE / heteroyohimbine synthase / medium chain dehydrogenase/reductase / NADP+ dependent enzyme / zinc binding site
Function / homology
Function and homology information


cinnamyl-alcohol dehydrogenase activity / lignin biosynthetic process / nucleotide binding / zinc ion binding
Similarity search - Function
: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal ...: / Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Polyketide synthase, enoylreductase domain / Enoylreductase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Tetrahydroalstonine synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsStavrinides, A. / Tatsis, E.C. / Caputi, L. / Foureau, E. / Stevenson, C.E.M. / Lawson, D.M. / Courdavault, V. / O'Connor, S.E.
Funding support United Kingdom, France, 4items
OrganizationGrant numberCountry
European Research Council311363 United Kingdom
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
Region CentreABISAL France
Biotechnology and Biological Sciences Research CouncilDoctoral Training Partnership United Kingdom
CitationJournal: Nat Commun / Year: 2016
Title: Structural investigation of heteroyohimbine alkaloid synthesis reveals active site elements that control stereoselectivity.
Authors: Stavrinides, A. / Tatsis, E.C. / Caputi, L. / Foureau, E. / Stevenson, C.E. / Lawson, D.M. / Courdavault, V. / O'Connor, S.E.
History
DepositionDec 22, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 27, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tetrahydroalstonine synthase
B: Tetrahydroalstonine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,63710
Polymers76,7642
Non-polymers1,8738
Water15,817878
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-34 kcal/mol
Surface area26570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.410, 112.310, 57.110
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-507-

HOH

21B-888-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: VAL / Beg label comp-ID: VAL / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 12 - 355 / Label seq-ID: 13 - 356

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

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Components

#1: Protein Tetrahydroalstonine synthase / heteroyohimbine synthase THAS1


Mass: 38381.977 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The native N-terminal MET is replaced by a GLY-PRO dipeptide remaining from affinity tag cleavage
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: A0A0F6SD02
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 878 / 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: 2.14 Å3/Da / Density % sol: 42.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.05→40.04 Å / Num. obs: 304642 / % possible obs: 99.7 % / Redundancy: 8.8 % / Biso Wilson estimate: 10.9 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.02 / Net I/σ(I): 15.4 / Num. measured all: 2684244
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
1.05-1.086.81.291.4148862217880.510.51796.9
4.7-40.048.30.04748.73082137170.9970.01799.8

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Processing

Software
NameVersionClassification
Aimless0.3.11data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
SHELXphasing
XDSdata reduction
RefinementMethod to determine structure: SAD / Resolution: 1.05→40.04 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.979 / WRfactor Rfree: 0.1389 / WRfactor Rwork: 0.1171 / FOM work R set: 0.8965 / SU B: 0.77 / SU ML: 0.017 / SU R Cruickshank DPI: 0.0224 / SU Rfree: 0.0232 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.022 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1434 15153 5 %RANDOM
Rwork0.123 ---
obs0.124 289489 99.73 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 133.69 Å2 / Biso mean: 17 Å2 / Biso min: 6.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.16 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.56 Å2
Refinement stepCycle: final / Resolution: 1.05→40.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5106 0 156 955 6217
Biso mean--13.1 31.53 -
Num. residues----688
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195871
X-RAY DIFFRACTIONr_bond_other_d0.0070.025577
X-RAY DIFFRACTIONr_angle_refined_deg1.6431.9818018
X-RAY DIFFRACTIONr_angle_other_deg1.3663.00212907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285786
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.46624.434212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81815992
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.891526
X-RAY DIFFRACTIONr_chiral_restr0.1070.2893
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217021
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021255
X-RAY DIFFRACTIONr_mcbond_it1.811.4242993
X-RAY DIFFRACTIONr_mcbond_other1.781.4222992
X-RAY DIFFRACTIONr_mcangle_it2.2992.1493802
X-RAY DIFFRACTIONr_rigid_bond_restr2.127311445
X-RAY DIFFRACTIONr_sphericity_free27.25245
X-RAY DIFFRACTIONr_sphericity_bonded11.893511988
Refine LS restraints NCS

Ens-ID: 1 / Number: 41438 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 1066 -
Rwork0.268 20698 -
all-21764 -
obs--96.91 %

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