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- PDB-5df1: Iridoid synthase from Catharanthus roseus - ternary complex with ... -

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Basic information

Entry
Database: PDB / ID: 5df1
TitleIridoid synthase from Catharanthus roseus - ternary complex with NADP+ and geranic 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
(2E)-3,7-dimethylocta-2,6-dienoic acid / IMIDAZOLE / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 26, 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 / 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)85,05212
Polymers82,8492
Non-polymers2,20310
Water9,296516
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,93510
Polymers82,8492
Non-polymers2,0868
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area5650 Å2
ΔGint3 kcal/mol
Surface area28850 Å2
MethodPISA
2
B: Iridoid synthase
hetero molecules

B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,16914
Polymers82,8492
Non-polymers2,32012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Buried area5260 Å2
ΔGint-3 kcal/mol
Surface area28790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.940, 95.470, 172.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: PRO / End label comp-ID: PRO / Refine code: _ / Auth seq-ID: 23 - 388 / Label seq-ID: 3 - 368

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

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Iridoid synthase


Mass: 41424.539 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.
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): SoluBL21 / References: UniProt: K7WDL7, EC: 1.3.1.99

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Non-polymers , 5 types, 526 molecules

#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-58X / (2E)-3,7-dimethylocta-2,6-dienoic acid


Mass: 168.233 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 46.07 %
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: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.75→66.22 Å / Num. obs: 76022 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 29 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7 / Num. measured all: 492160
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
1.75-1.86.61.6811.23650055010.5430.70298.1
7.83-66.225.80.0593155309510.9950.02799.8

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Processing

Software
NameVersionClassification
Aimless0.5.12data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DCU

5dcu


Resolution: 1.75→66.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / WRfactor Rfree: 0.2061 / WRfactor Rwork: 0.1757 / FOM work R set: 0.7581 / SU B: 7.892 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1256 / SU Rfree: 0.1156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 3887 5.1 %RANDOM
Rwork0.1868 ---
obs0.1882 72135 99.55 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 137.45 Å2 / Biso mean: 34.4 Å2 / Biso min: 18.84 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å20 Å2
2--1.97 Å20 Å2
3----2.7 Å2
Refinement stepCycle: final / Resolution: 1.75→66.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5736 0 145 523 6404
Biso mean--32.11 41.67 -
Num. residues----732
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0196184
X-RAY DIFFRACTIONr_bond_other_d0.0040.025724
X-RAY DIFFRACTIONr_angle_refined_deg1.3711.9418443
X-RAY DIFFRACTIONr_angle_other_deg1.052313228
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0415772
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46625.267262
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.744151005
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5051513
X-RAY DIFFRACTIONr_chiral_restr0.0830.2927
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0217247
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021406
X-RAY DIFFRACTIONr_mcbond_it1.5632.1442994
X-RAY DIFFRACTIONr_mcbond_other1.5632.1442993
X-RAY DIFFRACTIONr_mcangle_it2.213.2083759
Refine LS restraints NCS

Ens-ID: 1 / Number: 45496 / 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: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 307 -
Rwork0.366 5183 -
all-5490 -
obs--97.9 %
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)
11.44480.0132-0.26441.9512-0.081.90960.01580.1458-0.2116-0.1661-0.0643-0.13460.14060.08570.04860.0277-0.00210.01290.1162-0.03830.050111.090326.3687-18.6078
25.5808-2.4369-2.954810.1421-0.05356.72260.1468-0.4413-0.9004-0.0172-0.42421.1190.5875-1.01640.27740.1372-0.1825-0.03240.5070.03240.2082-9.182632.29260.1789
31.1242-0.28240.2150.9545-0.39731.3022-0.02460.0783-0.0432-0.0530.00050.07680.0124-0.11210.02410.0085-0.02460.00180.1441-0.03940.0176-2.765440.9789-15.4072
42.1110.0383-0.43481.04670.47932.3844-0.0061-0.18320.10420.1301-0.00880.1552-0.133-0.09610.01490.0350.00730.02050.1113-0.00030.041124.172959.7607-24.4445
52.45142.4768-4.69492.5037-4.74639.001-0.02110.190.096-0.02090.21280.09980.0749-0.4175-0.19170.4906-0.04710.06230.3994-0.00050.427426.672132.6765-38.8074
61.873-0.3059-0.24080.95930.00371.4724-0.1028-0.2564-0.17930.10820.02330.03150.11740.10180.07950.02660.01260.01840.10480.0170.024338.943646.4008-28.2027
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 153
2X-RAY DIFFRACTION2A154 - 168
3X-RAY DIFFRACTION3A169 - 388
4X-RAY DIFFRACTION4B23 - 153
5X-RAY DIFFRACTION5B154 - 160
6X-RAY DIFFRACTION6B161 - 388

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