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- PDB-5dcu: Iridoid synthase from Catharanthus roseus - ternary complex with ... -

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Basic information

Entry
Database: PDB / ID: 5dcu
TitleIridoid synthase from Catharanthus roseus - ternary complex with NADP+ and triethylene glycol carboxylic acid
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / Iridoid synthase / short chain dehydrogenase / NADPH-dependent / Catharanthus roseus
Function / homology
Function and homology information


(S)-8-oxocitronellyl enol synthase / monoterpenoid biosynthetic process / oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor / protein homodimerization activity / identical protein binding / cytosol
Similarity search - Function
NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / [2-(2-hydroxyethoxy)ethoxy]acetic acid / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsCaputi, L. / Kries, H. / Stevenson, C.E.M. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E.
Funding support United Kingdom, Switzerland, 3items
OrganizationGrant numberCountry
European Research Council311363 United Kingdom
Swiss National Science Foundation155581 Switzerland
Biotechnology and Biological Sciences Research CouncilBB/J004561/1 United Kingdom
CitationJournal: Nat.Chem.Biol. / Year: 2016
Title: Structural determinants of reductive terpene cyclization in iridoid biosynthesis.
Authors: Kries, H. / Caputi, L. / Stevenson, C.E. / Kamileen, M.O. / Sherden, N.H. / Geu-Flores, F. / Lawson, D.M. / O'Connor, S.E.
History
DepositionAug 24, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 28, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Dec 30, 2015Group: Database references
Revision 1.3Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_special_symmetry / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,60710
Polymers83,5442
Non-polymers2,0638
Water15,349852
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,60710
Polymers83,5442
Non-polymers2,0638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
2
B: Iridoid synthase
hetero molecules

B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,60710
Polymers83,5442
Non-polymers2,0638
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)92.030, 96.110, 172.630
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1237-

HOH

21A-1258-

HOH

31B-1242-

HOH

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

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PHE / End label comp-ID: PHE / Refine code: 0 / Auth seq-ID: 23 - 391 / Label seq-ID: 3 - 371

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

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Components

#1: Protein Iridoid synthase


Mass: 41771.969 Da / Num. of mol.: 2 / Fragment: UNP residues 23-388
Source method: isolated from a genetically manipulated source
Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87. The N- ...Details: The crystallised protein contained residues 23-388 of the wild-type amino acid sequence. The sequence differed from database entry K7WDL7 by an Asp to Asn change at position 87. The N-terminus retained two residues from the nickel affinity cleavage site. The C-terminus had an additional three vector-derived residues.
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 / References: UniProt: K7WDL7, EC: 1.3.1.99
#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
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-TEG / [2-(2-hydroxyethoxy)ethoxy]acetic acid


Mass: 164.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 852 / 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: 2.28 Å3/Da / Density % sol: 46.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop

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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: Jul 9, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.4→86.32 Å / Num. obs: 149766 / % possible obs: 100 % / Redundancy: 8.3 % / Biso Wilson estimate: 11.4 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.025 / Net I/σ(I): 16.1 / Num. measured all: 1249645
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
1.4-1.448.31.4471.590645109870.5690.53299.9
6.26-86.327.50.03351.31371618330.9980.01399.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
Aimless0.3.11data scaling
PDB_EXTRACT3.15data extraction
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6G

2v6g


Resolution: 1.4→86.32 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.172 / WRfactor Rwork: 0.148 / FOM work R set: 0.8783 / SU B: 2.005 / SU ML: 0.04 / SU R Cruickshank DPI: 0.055 / SU Rfree: 0.0571 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.055 / ESU R Free: 0.057 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1795 7213 4.8 %RANDOM
Rwork0.1549 ---
obs0.1561 142552 99.97 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 60.16 Å2 / Biso mean: 19.9 Å2 / Biso min: 9.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.38 Å20 Å2
3----0.4 Å2
Refinement stepCycle: final / Resolution: 1.4→86.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 134 869 6768
Biso mean--18.61 32.09 -
Num. residues----728
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0196451
X-RAY DIFFRACTIONr_bond_other_d0.0050.026003
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.9438844
X-RAY DIFFRACTIONr_angle_other_deg1.16313954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1365836
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49425.493284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.47151091
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9341514
X-RAY DIFFRACTIONr_chiral_restr0.0980.2966
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0217557
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021465
X-RAY DIFFRACTIONr_mcbond_it0.5971.0653087
X-RAY DIFFRACTIONr_mcbond_other0.5961.0653086
X-RAY DIFFRACTIONr_mcangle_it0.9731.5963896
Refine LS restraints NCS

Ens-ID: 1 / Number: 46448 / 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: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 504 -
Rwork0.321 10483 -
all-10987 -
obs--99.96 %
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)
10.8411-0.1951-0.10491.61750.23581.2156-0.04620.0454-0.1605-0.04910.0186-0.05440.07150.01310.02760.0216-0.01490.01350.0167-0.01180.03828.213127.0328-14.8168
20.9169-0.17090.18780.86160.04621.1936-0.07410.01150.091-0.00450.01680.0103-0.1875-0.07520.05730.0454-0.0031-0.0070.0196-0.0070.0139-4.12246.4477-14.3314
30.8277-0.02640.39760.6041-0.08661.7489-0.02480.1220.0184-0.08890.00720.0878-0.039-0.07060.01770.0445-0.0075-0.00760.0415-0.00750.022-4.033143.7909-21.2564
41.97450.185-0.20230.95740.16441.19510.042-0.1760.09370.0772-0.05120.0635-0.0794-0.01640.00920.0156-0.00690.00850.0227-0.01140.017624.287460.0898-24.7871
51.9001-0.3759-0.41010.7153-0.0090.9248-0.0338-0.0239-0.1641-0.0077-0.06260.06690.0245-0.00370.09650.0059-0.00070.00610.0088-0.00430.022934.910149.0709-33.0435
60.8975-0.1024-0.27490.5001-0.02331.9267-0.0713-0.255-0.2290.1434-0.0362-0.0260.13870.24040.10750.06210.01210.0190.11390.06970.082743.945744.4658-22.191
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 213
2X-RAY DIFFRACTION2A214 - 303
3X-RAY DIFFRACTION3A304 - 391
4X-RAY DIFFRACTION4B23 - 160
5X-RAY DIFFRACTION5B161 - 284
6X-RAY DIFFRACTION6B285 - 391

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