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- PDB-5dcy: Iridoid synthase G150A mutant from Catharanthus roseus - binary c... -

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Basic information

Entry
Database: PDB / ID: 5dcy
TitleIridoid synthase G150A mutant from Catharanthus roseus - binary complex with NADP+
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
: / PRISE-like Rossmann-fold domain / 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 / TRIETHYLENE GLYCOL / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 1.3Jun 8, 2016Group: Derived calculations
Revision 1.4Jan 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)85,03712
Polymers82,8772
Non-polymers2,16010
Water15,619867
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91310
Polymers82,8772
Non-polymers2,0358
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)85,16114
Polymers82,8772
Non-polymers2,28412
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)92.120, 95.900, 172.160
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-1258-

HOH

21A-1311-

HOH

31B-1206-

HOH

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

#1: Protein Iridoid synthase


Mass: 41438.566 Da / Num. of mol.: 2 / Fragment: 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 and by a Gly ...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 and by a Gly to Ala change at position 150. The N-terminus retained two residues from the nickel affinity cleavage site.
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pOPIN-F / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): soluBl21 / References: UniProt: K7WDL7, EC: 1.3.1.99
#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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 867 / 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: 2.29 Å3/Da / Density % sol: 46.38 %
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: 0.9173 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 26, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.45→41.89 Å / Num. obs: 134019 / % possible obs: 99.7 % / Redundancy: 8.2 % / Biso Wilson estimate: 14.2 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Rpim(I) all: 0.04 / Net I/σ(I): 11.4 / Num. measured all: 1102473
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
1.45-1.497.61.5921.37230095510.5220.61297.1
6.48-41.897.80.04237.11286516420.9990.01699.5

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Processing

Software
NameVersionClassification
Aimless0.5.9data scaling
REFMAC5.8.0107refinement
PDB_EXTRACT3.15data extraction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5DCU

5dcu


Resolution: 1.45→41.89 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.964 / WRfactor Rfree: 0.1769 / WRfactor Rwork: 0.158 / FOM work R set: 0.8432 / SU B: 2.767 / SU ML: 0.053 / SU R Cruickshank DPI: 0.0661 / SU Rfree: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.066 / ESU R Free: 0.065 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1873 6807 5.1 %RANDOM
Rwork0.1682 ---
obs0.1692 127212 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 65.4 Å2 / Biso mean: 20.9 Å2 / Biso min: 9.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.09 Å20 Å20 Å2
2--1.01 Å20 Å2
3----0.91 Å2
Refinement stepCycle: final / Resolution: 1.45→41.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5687 0 140 893 6720
Biso mean--20.29 31.57 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196329
X-RAY DIFFRACTIONr_bond_other_d0.0050.025851
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9438675
X-RAY DIFFRACTIONr_angle_other_deg1.183313578
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2575816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04625.495273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.568151050
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1571514
X-RAY DIFFRACTIONr_chiral_restr0.0960.2950
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217442
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021428
X-RAY DIFFRACTIONr_mcbond_it0.9531.0613065
X-RAY DIFFRACTIONr_mcbond_other0.9511.0613064
X-RAY DIFFRACTIONr_mcangle_it1.4261.5923882
Refine LS restraints NCS

Ens-ID: 1 / Number: 45184 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.45→1.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.31 485 -
Rwork0.315 9055 -
all-9540 -
obs--97.15 %
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)
11.1477-0.1014-0.10291.93770.14251.6884-0.01170.0638-0.185-0.0454-0.0166-0.01160.0665-0.05380.02830.0313-0.01110.00190.0161-0.0170.03617.817326.3369-14.3986
21.0688-0.21540.25630.5436-0.1521.5672-0.02210.1203-0.002-0.05850.01730.048-0.0128-0.06350.00490.0404-0.02550.00520.0341-0.00480.0095-4.041244.1574-17.6837
31.8510.0777-0.381.00330.03651.22660.0392-0.17560.15330.1024-0.01490.0742-0.0856-0.0004-0.02430.0255-0.01270.00920.0315-0.01430.017424.167560.5693-24.203
48.4232-0.5955-0.140211.4786-0.46760.0447-0.13070.565-1.0382-0.88990.11160.82840.0989-0.05680.01910.2364-0.10640.02320.1796-0.09440.203932.871543.19-45.5005
53.1748-1.0231-0.94163.74970.0612.624-0.0040.2606-0.192-0.1805-0.02970.39110.0587-0.23920.03370.015-0.0127-0.01730.0724-0.01380.043719.558452.0061-39.0979
61.4958-0.3964-0.5370.90880.19451.3536-0.0894-0.3296-0.14040.15650.0284-0.01180.13930.23310.0610.05160.01020.00750.09520.03220.018642.378345.5193-25.7328
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A23 - 200
2X-RAY DIFFRACTION2A201 - 388
3X-RAY DIFFRACTION3B23 - 149
4X-RAY DIFFRACTION4B150 - 168
5X-RAY DIFFRACTION5B169 - 198
6X-RAY DIFFRACTION6B199 - 388

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