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- PDB-5h82: HETEROYOHIMBINE SYNTHASE THAS2 FROM CATHARANTHUS ROSEUS - APO FORM -

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Basic information

Entry
Database: PDB / ID: 5h82
TitleHETEROYOHIMBINE SYNTHASE THAS2 FROM CATHARANTHUS ROSEUS - APO FORM
Componentsheteroyohimbine synthase THAS2
KeywordsOXIDOREDUCTASE / heteroyohimbine synthase / medium chain dehydrogenase/reductase / NADP+ dependent enzyme / zinc binding site
Function / homology
Function and homology information


alkaloid metabolic process / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / nucleotide binding / metal ion binding
Similarity search - Function
: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily ...: / Quinone Oxidoreductase; Chain A, domain 1 / Medium-chain alcohol dehydrogenases, catalytic domain / Alcohol dehydrogenase-like, C-terminal / Zinc-binding dehydrogenase / 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
Heteroyohimbine synthase THAS2
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 grant 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 23, 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 1.2Jan 10, 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 / 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: heteroyohimbine synthase THAS2
B: heteroyohimbine synthase THAS2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,4996
Polymers85,2382
Non-polymers2624
Water5,765320
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-12 kcal/mol
Surface area28280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.360, 88.080, 121.390
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: LYS / End label comp-ID: LYS / Refine code: _ / Auth seq-ID: 8 - 369 / Label seq-ID: 26 - 387

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

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Components

#1: Protein heteroyohimbine synthase THAS2


Mass: 42618.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Native N-terminal MET is replaced by an affinity tag with the sequence MAHHHHHHSSGLEVLFQGP Ignore Uniprot information below
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: A0A1C7D193*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: NULL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Aug 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.05→60.69 Å / Num. obs: 49345 / % possible obs: 99.9 % / Redundancy: 18.8 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.033 / Net I/σ(I): 17 / Num. measured all: 928074
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
2.05-2.119.21.8821.96846035700.6390.43999.9
9.17-60.6917.40.03569.51109363810.00999.6

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Processing

Software
NameVersionClassification
Aimless0.5.7data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5H81

5h81


Resolution: 2.05→60.69 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.911 / WRfactor Rfree: 0.1992 / WRfactor Rwork: 0.1686 / FOM work R set: 0.8345 / SU B: 8.66 / SU ML: 0.122 / SU R Cruickshank DPI: 0.1815 / SU Rfree: 0.1606 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.182 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2254 2516 5.1 %RANDOM
Rwork0.1862 ---
obs0.1882 46829 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 127.8 Å2 / Biso mean: 43.3 Å2 / Biso min: 21.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å20 Å2
2---1.03 Å20 Å2
3---0.35 Å2
Refinement stepCycle: final / Resolution: 2.05→60.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5107 0 4 320 5431
Biso mean--39.68 42.37 -
Num. residues----675
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0195265
X-RAY DIFFRACTIONr_bond_other_d0.0050.025030
X-RAY DIFFRACTIONr_angle_refined_deg1.4881.9697123
X-RAY DIFFRACTIONr_angle_other_deg1.1723.00211573
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2465673
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.81223.869199
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.96415862
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.8071522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2801
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215885
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021147
X-RAY DIFFRACTIONr_mcbond_it2.2092.3612707
X-RAY DIFFRACTIONr_mcbond_other2.2092.362706
X-RAY DIFFRACTIONr_mcangle_it3.1463.5193375
Refine LS restraints NCS

Ens-ID: 1 / Number: 39490 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 183 -
Rwork0.268 3381 -
all-3564 -
obs--99.78 %
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)
14.7905-0.15450.30452.55560.06931.49060.0510.21470.0956-0.1623-0.04490.17510.1526-0.0147-0.00610.0504-0.0169-0.00190.0257-0.00620.019-10.7395-32.65814.8618
26.00171.325-5.6843.8172-3.64357.2594-0.06690.53880.2224-0.44030.2313-0.09430.2004-0.4101-0.16440.1886-0.0890.01510.2018-0.02570.0857-4.6034-23.35511.3095
30.3461.06530.21113.7330.80991.25960.0398-0.01660.10.107-0.13020.1683-0.15480.01850.09030.0345-0.01380.00650.0909-0.00410.0884-3.6892-11.284721.2179
40.78120.0573-0.19776.1565-1.44252.42360.04160.19580.187-0.0988-0.04670.488-0.4689-0.2590.00510.14420.012-0.01190.1804-0.01360.1451-2.5191-1.389412.9695
55.33192.88330.63542.53870.04293.09780.2496-0.2130.74520.6137-0.26190.5415-0.0679-0.16130.01230.2455-0.08080.1070.0767-0.07950.1654-15.8991-22.746926.544
62.6950.15940.39355.4927-0.63752.8296-0.1548-0.34520.2730.80340.37110.0827-0.425-0.1087-0.21630.19180.1065-0.00460.1423-0.01560.1136-5.358532.2881-11.9628
70.6817-1.3125-0.04755.563-1.46281.3221-0.1516-0.20260.08920.3680.1466-0.2061-0.1203-0.04790.00510.0620.0591-0.05070.1811-0.0250.13131.085515.8227-11.1812
81.48210.08170.1064.7698-0.26316.13250.00760.0770.017-0.50540.0940.70030.1597-0.8829-0.10160.1485-0.0138-0.06270.27150.02090.2197-4.5741-4.157-13.5331
90.0928-0.46310.2034.6443-2.53591.8522-0.0665-0.0934-0.02440.05820.2656-0.01420.1512-0.1521-0.19910.09620.0507-0.03940.18940.00640.2054-2.737212.8193-13.5021
105.5358-2.2438-0.548310.8784-0.14267.9341-0.0995-0.0307-0.1056-0.51930.28240.32960.0509-0.0906-0.18290.0462-0.0187-0.04110.16080.0490.0748-8.834526.7306-24.7473
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 96
2X-RAY DIFFRACTION2A97 - 143
3X-RAY DIFFRACTION3A144 - 250
4X-RAY DIFFRACTION4A251 - 330
5X-RAY DIFFRACTION5A331 - 370
6X-RAY DIFFRACTION6B8 - 103
7X-RAY DIFFRACTION7B104 - 229
8X-RAY DIFFRACTION8B230 - 299
9X-RAY DIFFRACTION9B300 - 353
10X-RAY DIFFRACTION10B354 - 371

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