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- PDB-5dbg: Crystal Structure of Iridoid Synthase from Cantharanthus roseus i... -

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Basic information

Entry
Database: PDB / ID: 5dbg
TitleCrystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / metal-binding / substrate binding / acidocalcisomal pyrophosphatase / inhibitor
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLiu, W.D. / Hu, Y.M. / Zheng, Y.Y. / Xu, Z.X. / Ko, T.P. / Chen, C.C. / Guo, R.T.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2015
Title: Structures of Iridoid Synthase from Cantharanthus roseus with Bound NAD(+) , NADPH, or NAD(+) /10-Oxogeranial: Reaction Mechanisms
Authors: Hu, Y.M. / Liu, W.D. / Malwal, S.R. / Zheng, Y.Y. / Feng, X.X. / Ko, T.P. / Chen, C.C. / Xu, Z.X. / Liu, M.X. / Han, X. / Gao, J. / Oldfield, E. / Guo, R.T.
History
DepositionAug 21, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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)85,8944
Polymers84,5672
Non-polymers1,3272
Water10,106561
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8944
Polymers84,5672
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
Buried area4460 Å2
ΔGint-17 kcal/mol
Surface area28490 Å2
MethodPISA
2
B: Iridoid synthase
hetero molecules

B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,8944
Polymers84,5672
Non-polymers1,3272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4490 Å2
ΔGint-20 kcal/mol
Surface area29050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.124, 95.583, 173.036
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-676-

HOH

21A-761-

HOH

31B-543-

HOH

41B-664-

HOH

51B-730-

HOH

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

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 26 - 390 / Label seq-ID: 1 - 365

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

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Components

#1: Protein Iridoid synthase


Mass: 42283.418 Da / Num. of mol.: 2 / Fragment: UNP residues 26-388
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Catharanthus roseus (Madagascar periwinkle)
Plasmid: pET32Xa/LIC / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.31 Å3/Da / Density % sol: 46.73 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: Ammonium Acetate, Sodium Acetate trihydrate, Polyethylene Glycol 4000, Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2015
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→25 Å / Num. obs: 54153 / % possible obs: 96.5 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.059 / Rrim(I) all: 0.121 / Χ2: 1.418 / Net I/av σ(I): 15.453 / Net I/σ(I): 9.6 / Num. measured all: 212900
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-2.023.10.49951830.7850.3040.5880.65793.7
2.02-2.13.60.41453270.8490.2420.4820.7996.2
2.1-2.240.33453790.9050.1860.3840.93896.9
2.2-2.314.10.29953970.9350.1640.3431.33896.7
2.31-2.464.20.20854100.9640.1130.2381.34597.1
2.46-2.654.20.16854450.9760.0910.1921.65397.3
2.65-2.914.20.12754480.9850.0680.1451.7397.3
2.91-3.334.10.08654870.9930.0470.0981.92497.3
3.33-4.240.06454810.9930.0360.0741.72496.5
4.2-253.80.06255960.9930.0350.0721.68995.6

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6F

2v6f


Resolution: 1.95→25 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.934 / WRfactor Rfree: 0.2273 / WRfactor Rwork: 0.1747 / FOM work R set: 0.8223 / SU B: 4.181 / SU ML: 0.117 / SU R Cruickshank DPI: 0.1759 / SU Rfree: 0.162 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.176 / ESU R Free: 0.162 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2295 2698 5 %RANDOM
Rwork0.1769 ---
obs0.1795 51397 95.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 107.09 Å2 / Biso mean: 27.46 Å2 / Biso min: 13.79 Å2
Baniso -1Baniso -2Baniso -3
1--0.45 Å2-0 Å2-0 Å2
2--1.83 Å20 Å2
3----1.39 Å2
Refinement stepCycle: final / Resolution: 1.95→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5723 0 88 561 6372
Biso mean--20.67 35.38 -
Num. residues----721
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0195967
X-RAY DIFFRACTIONr_bond_other_d0.0060.025603
X-RAY DIFFRACTIONr_angle_refined_deg1.9161.968112
X-RAY DIFFRACTIONr_angle_other_deg1.261312952
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5275717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.0325.156256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.954151009
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8421514
X-RAY DIFFRACTIONr_chiral_restr0.1430.2894
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0216609
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021347
X-RAY DIFFRACTIONr_mcbond_it2.2122.4762879
X-RAY DIFFRACTIONr_mcbond_other2.2092.4752878
X-RAY DIFFRACTIONr_mcangle_it3.0743.6983593
Refine LS restraints NCS

Ens-ID: 1 / Number: 21902 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.95→1.99 Å
RfactorNum. reflection% reflection
Rfree0.271 164 -
Rwork0.241 3214 -
obs--82.49 %

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