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- PDB-8a3n: Geissoschizine synthase from Catharanthus roseus - binary complex... -

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Basic information

Entry
Database: PDB / ID: 8a3n
TitleGeissoschizine synthase from Catharanthus roseus - binary complex with NADP+
ComponentsGeissoschizine synthase
KeywordsOXIDOREDUCTASE / medium-chain alcohol dehydrogenase / iminium reduction / natural product biosynthesis
Function / homology
Function and homology information


geissoschizine dehydrogenase / geissoschizine dehydrogenase activity / indole alkaloid metabolic process / response to silver ion / response to jasmonic acid / zinc ion binding
Similarity search - Function
Alcohol dehydrogenase, zinc-type, conserved site / Zinc-containing alcohol dehydrogenases signature. / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / Polyketide synthase, enoylreductase domain / Enoylreductase / GroES-like superfamily / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Geissoschizine synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLangley, C. / Tatsis, E. / Hong, B. / Nakamura, Y. / Kamileen, M.O. / Paetz, C. / Stevenson, C.E.M. / Basquin, J. / Lawson, D.M. / Caputi, L. / O'Connor, S.E.
Funding supportEuropean Union, United Kingdom, 2items
OrganizationGrant numberCountry
European Research Council (ERC)788301European Union
Biotechnology and Biological Sciences Research Council (BBSRC)BB/P012523/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Expansion of the Catalytic Repertoire of Alcohol Dehydrogenases in Plant Metabolism.
Authors: Langley, C. / Tatsis, E. / Hong, B. / Nakamura, Y. / Paetz, C. / Stevenson, C.E.M. / Basquin, J. / Lawson, D.M. / Caputi, L. / O'Connor, S.E.
History
DepositionJun 8, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 19, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 30, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)80,9248
Polymers79,1752
Non-polymers1,7486
Water5,026279
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.383, 100.969, 66.681
Angle α, β, γ (deg.)90.000, 106.780, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Geissoschizine synthase / CrGS / Alcohol dehydrogenase 14 / CrADH14


Mass: 39587.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Native N-terminal MET is replaced by a GLY-PRO dipeptide left over from cleavage of the affinity tag
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Gene: GS, ADH14, Caros006689 / Plasmid: POPINF / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: W8JWW7, geissoschizine dehydrogenase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE / Nicotinamide adenine dinucleotide phosphate


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


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 279 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.26 Å3/Da / Density % sol: 45.5 % / Description: NULL
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: NULL

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2→63.84 Å / Num. obs: 46753 / % possible obs: 98.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 19.2 Å2 / CC1/2: 0.986 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.075 / Rrim(I) all: 0.188 / Net I/σ(I): 9.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.056.50.9462212234060.6480.4091.0323.296.8
8.94-63.845.70.1430505390.9640.0640.15417.396.6

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimless0.5.31data scaling
REFMAC5.8.0350refinement
PDB_EXTRACT3.27data extraction
PHASER2.7.17phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FI3

5fi3


Resolution: 2→63.84 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.928 / SU B: 8.709 / SU ML: 0.128 / SU R Cruickshank DPI: 0.2123 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 2334 5 %RANDOM
Rwork0.2054 ---
obs0.2067 44395 98.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.16 Å2 / Biso mean: 27.11 Å2 / Biso min: 12.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å20 Å2-0.92 Å2
2--3.44 Å20 Å2
3----1.26 Å2
Refinement stepCycle: final / Resolution: 2→63.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5219 0 100 279 5598
Biso mean--23.98 32.44 -
Num. residues----703
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0125451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165029
X-RAY DIFFRACTIONr_angle_refined_deg1.0651.6387376
X-RAY DIFFRACTIONr_angle_other_deg0.3541.55811682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3425703
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.6841023
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.44710878
X-RAY DIFFRACTIONr_chiral_restr0.0490.2826
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026145
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021061
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.413 170 -
Rwork0.401 3225 -
all-3395 -
obs--96.42 %
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)
11.5867-0.1909-0.92710.56530.21291.669-0.0165-0.0320.0195-0.0740.0873-0.0137-0.12210.128-0.07070.0592-0.0163-0.0210.0246-0.01310.0278-20.511923.9425-1.0001
22.071-0.8098-0.60590.91390.43571.0618-0.0061-0.180.03670.0531-0.0101-0.03520.00040.13680.01620.0139-0.0116-0.00910.04230.00620.0074-3.3349-0.8668-32.3456
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 999
2X-RAY DIFFRACTION2B0 - 999

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