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- PDB-5h83: HETEROYOHIMBINE SYNTHASE HYS FROM CATHARANTHUS ROSEUS - APO FORM -

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Basic information

Entry
Database: PDB / ID: 5h83
TitleHETEROYOHIMBINE SYNTHASE HYS FROM CATHARANTHUS ROSEUS - APO FORM
Componentsheteroyohimbine synthase HYS
KeywordsOXIDOREDUCTASE / heteroyohimbine synthase / medium chain dehydrogenase/reductase / NADP+ dependent enzyme / zinc binding site
Function / homology
Function and homology information


oxidoreductase activity / 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 / Alcohol dehydrogenase, N-terminal / Alcohol dehydrogenase GroES-like domain / GroES-like superfamily / NAD(P)-binding Rossmann-like Domain ...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 / 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 HYS
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: heteroyohimbine synthase HYS
B: heteroyohimbine synthase HYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,6296
Polymers77,3672
Non-polymers2624
Water3,243180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2490 Å2
ΔGint-21 kcal/mol
Surface area27800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.630, 188.630, 58.950
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4

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Components

#1: Protein heteroyohimbine synthase HYS


Mass: 38683.633 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: Cr_032583b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SOLUBL21 / References: UniProt: A0A1C7D195*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 / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 3.39 Å3/Da / Density % sol: 63.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / 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 6M / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.25→48.32 Å / Num. obs: 49387 / % possible obs: 99.7 % / Redundancy: 5.1 % / Biso Wilson estimate: 31.6 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.14 / Rpim(I) all: 0.068 / Net I/σ(I): 9.1 / Num. measured all: 251519
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allCC1/2Rpim(I) all% possible all
2.25-2.3151.3661.11758435450.510.66497.8
10.06-48.324.60.0340.927866000.9990.01599.1

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Processing

Software
NameVersionClassification
Aimless0.5.8data scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FI3

5fi3


Resolution: 2.25→48.32 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.2242 / WRfactor Rwork: 0.1902 / FOM work R set: 0.8312 / SU B: 12.478 / SU ML: 0.147 / SU R Cruickshank DPI: 0.2024 / SU Rfree: 0.1748 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.202 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2242 2536 5.1 %RANDOM
Rwork0.1902 ---
obs0.192 46849 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 133.17 Å2 / Biso mean: 52.8 Å2 / Biso min: 18.64 Å2
Baniso -1Baniso -2Baniso -3
1-1.8 Å20 Å20 Å2
2--1.8 Å20 Å2
3----3.59 Å2
Refinement stepCycle: final / Resolution: 2.25→48.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5217 0 4 180 5401
Biso mean--51.89 42.3 -
Num. residues----704
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0195365
X-RAY DIFFRACTIONr_bond_other_d0.0020.025097
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.9717268
X-RAY DIFFRACTIONr_angle_other_deg0.9533.00211740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5955706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.79524.926203
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.68715857
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6561514
X-RAY DIFFRACTIONr_chiral_restr0.0760.2822
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021157
X-RAY DIFFRACTIONr_mcbond_it3.2082.6452824
X-RAY DIFFRACTIONr_mcbond_other3.2082.6452823
X-RAY DIFFRACTIONr_mcangle_it4.3593.9563530
LS refinement shellResolution: 2.25→2.309 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 156 -
Rwork0.324 3379 -
all-3535 -
obs--97.87 %
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)
11.0989-2.1361-0.78436.36652.31543.0459-0.1083-0.2118-0.22730.41840.1234-0.1520.81710.0265-0.01510.2312-0.0112-0.02320.13860.09440.2184-40.786930.974721.573
21.266-0.8552-1.02033.62731.19763.82640.06850.0605-0.032-0.0311-0.0053-0.5910.23290.317-0.06310.04490.0202-0.01360.07260.00680.1316-37.42236.837812.9088
35.83190.14460.04620.95350.26431.75130.0376-0.05830.23780.0310.0271-0.32120.020.5917-0.06470.024-0.0167-0.00350.2245-0.00860.1239-29.804247.134414.9904
42.38471.7892-0.57331.5925-0.08065.128-0.0429-0.1184-0.13050.0399-0.0526-0.19740.24980.34670.09550.02920.0131-0.01260.043-0.010.0673-37.357343.48229.3269
54.78820.38350.29211.1748-0.10621.76530.09990.3296-0.2767-0.079-0.0536-0.34390.19290.3972-0.04630.04060.00890.02940.3062-0.01590.1615-22.759942.149-13.4544
62.2170.2693-0.27443.47340.07293.1913-0.0431-0.0212-0.1936-0.09580.0517-0.14460.31050.1501-0.00860.03330.01320.00410.0078-0.00140.0214-40.363237.24631.6641
7100.0756-109.6494-74.1844121.59596.1829207.5182-1.30670.8002-0.76791.7834-1.08171.01714.5555-2.69422.38840.4572-0.04810.09250.38770.01730.438415.208264.895-34.869
83.6637-1.22051.23521.5413-0.93252.3190.29990.80870.5615-0.5132-0.17990.2036-0.1913-0.2672-0.120.37790.0940.03020.68960.1280.367111.817459.3154-20.8731
95.7006-0.5427-1.89320.07550.22672.3925-0.10630.16820.0655-0.02890.0528-0.04480.2179-0.12040.05350.3659-0.02140.01160.38060.00330.3911.474955.4018-22.3531
104.0150.3201-0.68011.9961-0.26162.93490.0937-0.18450.3621-0.0666-0.124-0.0409-0.2511-0.22860.03030.03590.0525-0.01580.4245-0.07480.25387.024254.5353-1.3866
116.40060.0866-1.80053.09930.23053.97350.0421-0.4352-0.66820.1721-0.1398-0.16250.6096-0.00320.09770.1194-0.0186-0.00270.56660.01430.3478-2.276139.70614.0883
124.42950.4409-0.68850.7957-0.04850.56160.13470.27310.2935-0.0855-0.00560.0575-0.1839-0.1973-0.12910.11840.0555-0.00840.4480.00210.158610.254751.0822-7.5507
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 39
2X-RAY DIFFRACTION2A40 - 87
3X-RAY DIFFRACTION3A88 - 125
4X-RAY DIFFRACTION4A126 - 170
5X-RAY DIFFRACTION5A171 - 298
6X-RAY DIFFRACTION6A299 - 357
7X-RAY DIFFRACTION7B6 - 10
8X-RAY DIFFRACTION8B11 - 114
9X-RAY DIFFRACTION9B115 - 131
10X-RAY DIFFRACTION10B132 - 225
11X-RAY DIFFRACTION11B226 - 279
12X-RAY DIFFRACTION12B280 - 359

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