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- PDB-5coa: Crystal structure of iridoid synthase at 2.2-angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 5coa
TitleCrystal structure of iridoid synthase at 2.2-angstrom resolution
ComponentsIridoid synthase
KeywordsOXIDOREDUCTASE / SDR / P5bR / Rossmann fold / 1-4 addition
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
(S)-8-oxocitronellyl enol synthase
Similarity search - Component
Biological speciesCatharanthus roseus (Madagascar periwinkle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsQin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
CitationJournal: J.Struct.Biol. / Year: 2016
Title: Structure of iridoid synthase in complex with NADP(+)/8-oxogeranial reveals the structural basis of its substrate specificity.
Authors: Qin, L. / Zhu, Y. / Ding, Z. / Zhang, X. / Ye, S. / Zhang, R.
History
DepositionJul 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 30, 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
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

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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)83,0957
Polymers82,4292
Non-polymers6675
Water7,819434
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3340 Å2
ΔGint-74 kcal/mol
Surface area30610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.290, 160.290, 85.576
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number94
Space group name H-MP42212

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Components

#1: Protein Iridoid synthase


Mass: 41214.305 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)
Production host: Escherichia coli (E. coli) / References: UniProt: K7WDL7, EC: 1.3.1.99
#2: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.33 Å3/Da / Density % sol: 63.11 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M HEPES pH 7.5, 1.98 M ammonium sulfate, 1% PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.2→38.9 Å / Num. obs: 56895 / % possible obs: 99.4 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 7
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 9.3 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2V6G

2v6g


Resolution: 2.2→38.9 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2879 5.07 %
Rwork0.1746 --
obs0.1763 56809 99.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→38.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5658 0 39 434 6131
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055846
X-RAY DIFFRACTIONf_angle_d0.9237933
X-RAY DIFFRACTIONf_dihedral_angle_d12.1782126
X-RAY DIFFRACTIONf_chiral_restr0.062869
X-RAY DIFFRACTIONf_plane_restr0.004999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1968-2.23280.25491190.21762520X-RAY DIFFRACTION99
2.2328-2.27130.28571400.2032526X-RAY DIFFRACTION99
2.2713-2.31260.23491330.19572531X-RAY DIFFRACTION100
2.3126-2.35710.23871420.19152546X-RAY DIFFRACTION100
2.3571-2.40520.23771360.18692530X-RAY DIFFRACTION100
2.4052-2.45750.24121370.18462538X-RAY DIFFRACTION99
2.4575-2.51470.21151310.18112563X-RAY DIFFRACTION100
2.5147-2.57750.23481360.17762546X-RAY DIFFRACTION100
2.5775-2.64720.21751340.18272537X-RAY DIFFRACTION100
2.6472-2.72510.23461510.18142553X-RAY DIFFRACTION100
2.7251-2.8130.21831280.18072504X-RAY DIFFRACTION97
2.813-2.91350.2361290.18642567X-RAY DIFFRACTION100
2.9135-3.03010.22061340.1812584X-RAY DIFFRACTION100
3.0301-3.1680.22651160.17812603X-RAY DIFFRACTION100
3.168-3.33490.18621400.17242570X-RAY DIFFRACTION100
3.3349-3.54370.17961470.16242597X-RAY DIFFRACTION100
3.5437-3.81710.17861630.15492565X-RAY DIFFRACTION100
3.8171-4.20080.17191360.15652520X-RAY DIFFRACTION96
4.2008-4.80780.19731260.14932655X-RAY DIFFRACTION100
4.8078-6.05360.21011420.18192664X-RAY DIFFRACTION100
6.0536-100.20291590.18942711X-RAY DIFFRACTION97
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)
14.40030.3892-0.07472.20910.54934.25630.02380.3531-0.0006-0.22170.0851-0.255-0.31060.3519-0.1210.2528-0.06270.01630.18530.01120.20233.031459.009137.7467
22.36510.6042-0.28122.29880.67382.4014-0.0153-0.1193-0.25670.1328-0.0553-0.11440.0110.1010.09070.20430.04050.03430.18710.01130.181224.652946.737347.8128
31.1076-0.4479-0.61821.88051.19372.28980.01810.1682-0.123-0.1207-0.1378-0.0315-0.0182-0.15540.12860.14640.02340.03370.17920.00760.174219.474239.12327.9749
42.835-0.7502-0.55181.656-0.14210.831-0.03320.5509-0.5289-0.0565-0.09560.46480.109-0.39240.10110.208-0.0242-0.00670.5527-0.15050.3291-20.391345.322837.8045
51.2846-0.1677-0.3991.44-1.01452.331-0.14770.0586-0.30650.1214-0.01240.06790.157-0.27230.14850.2058-0.0450.08320.2397-0.06570.2582-5.498934.998452.0721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 27 through 129 )
2X-RAY DIFFRACTION2chain 'A' and (resid 130 through 214 )
3X-RAY DIFFRACTION3chain 'A' and (resid 215 through 387 )
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 214 )
5X-RAY DIFFRACTION5chain 'B' and (resid 215 through 387 )

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