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

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Basic information

Entry
Database: PDB / ID: 5dbi
TitleCrystal Structure of Iridoid Synthase from Cantharanthus roseus in complex with NAD+ and 10-oxogeranial
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
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
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / (2E,6E)-2,6-dimethylocta-2,6-dienedial / (S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsHu, Y.M. / Liu, W.D. / 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)86,2266
Polymers84,5672
Non-polymers1,6594
Water3,945219
1
A: Iridoid synthase
hetero molecules

A: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2266
Polymers84,5672
Non-polymers1,6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_455-x-1,y,-z+1/21
2
B: Iridoid synthase
hetero molecules

B: Iridoid synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2266
Polymers84,5672
Non-polymers1,6594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)92.056, 94.629, 172.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-581-

HOH

21B-604-

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: Chemical ChemComp-XOG / (2E,6E)-2,6-dimethylocta-2,6-dienedial / 8-oxogeranial


Mass: 166.217 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H14O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 219 / 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: 46.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging 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: 2.2→25 Å / Num. obs: 41981 / % possible obs: 99.7 % / Redundancy: 4.2 % / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.026 / Rrim(I) all: 0.055 / Χ2: 0.771 / Net I/av σ(I): 28.499 / Net I/σ(I): 10.4 / Num. measured all: 161798
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.284.10.32937270.9290.1790.3750.62598.3
2.28-2.374.30.24838280.9610.1350.2840.51299.9
2.37-2.484.30.18337850.9750.0990.2090.514100
2.48-2.614.30.13938110.9860.0760.1590.52699.9
2.61-2.774.30.09938340.9920.0540.1130.544100
2.77-2.984.30.07238390.9950.0390.0820.58699.8
2.98-3.284.20.04738520.9980.0260.0540.63899.9
3.28-3.764.20.0438570.9980.0220.0460.907100
3.76-4.734.10.04439030.9970.0250.0511.899.9
4.73-2540.0340250.9980.0170.0341.11299.5

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Processing

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

2v6f


Resolution: 2.2→25 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.975 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.259 / ESU R Free: 0.192 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.20989 1945 5.1 %RANDOM
Rwork0.16348 ---
obs0.1658 36479 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.254 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å2-0 Å2
2--2.98 Å20 Å2
3----2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5741 0 112 219 6072
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0196007
X-RAY DIFFRACTIONr_bond_other_d0.0040.025643
X-RAY DIFFRACTIONr_angle_refined_deg1.7631.9628160
X-RAY DIFFRACTIONr_angle_other_deg1.0443.00113042
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855719
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.41225.194258
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.063151013
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7041514
X-RAY DIFFRACTIONr_chiral_restr0.1150.2896
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0216655
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021357
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.0574.722888
X-RAY DIFFRACTIONr_mcbond_other4.0584.7182887
X-RAY DIFFRACTIONr_mcangle_it5.7047.053603
X-RAY DIFFRACTIONr_mcangle_other5.7047.0523604
X-RAY DIFFRACTIONr_scbond_it4.9315.1913119
X-RAY DIFFRACTIONr_scbond_other4.935.1913120
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.2427.5614558
X-RAY DIFFRACTIONr_long_range_B_refined9.01538.2887108
X-RAY DIFFRACTIONr_long_range_B_other9.01638.2317063
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 22291 / 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: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 131 -
Rwork0.279 2560 -
obs--97.39 %

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