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- PDB-8yj4: The complex structure of SdnG with its analogue of substrate -

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Basic information

Entry
Database: PDB / ID: 8yj4
TitleThe complex structure of SdnG with its analogue of substrate
ComponentsSordarin/hypoxysordarin biosynthesis cluster protein G
KeywordsBIOSYNTHETIC PROTEIN / Diels Alderase / Norbornene / Sordarin / Analogue
Function / homologySnoaL-like domain / SnoaL-like domain / antibiotic biosynthetic process / NTF2-like domain superfamily / : / Sordarin/hypoxysordarin biosynthesis cluster protein G
Function and homology information
Biological speciesSordaria araneosa (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, J. / Zang, X. / Yi, T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Catal / Year: 2025
Title: Iminium Catalysis in Natural Diels-Alderase.
Authors: Sun, Z. / Zang, X. / Zhou, Q. / Ohashi, M. / Houk, K.N. / Zhou, J. / Tang, Y.
History
DepositionMar 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sordarin/hypoxysordarin biosynthesis cluster protein G
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
C: Sordarin/hypoxysordarin biosynthesis cluster protein G
D: Sordarin/hypoxysordarin biosynthesis cluster protein G
E: Sordarin/hypoxysordarin biosynthesis cluster protein G
F: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,71312
Polymers97,8026
Non-polymers1,9116
Water5,441302
1
A: Sordarin/hypoxysordarin biosynthesis cluster protein G
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2384
Polymers32,6012
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-18 kcal/mol
Surface area12420 Å2
MethodPISA
2
C: Sordarin/hypoxysordarin biosynthesis cluster protein G
D: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2384
Polymers32,6012
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3800 Å2
ΔGint-18 kcal/mol
Surface area12400 Å2
MethodPISA
3
E: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules

F: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2384
Polymers32,6012
Non-polymers6372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555-x+1/2,y+1/2,-z1
Buried area3880 Å2
ΔGint-18 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.960, 111.210, 81.590
Angle α, β, γ (deg.)90.000, 113.026, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein
Sordarin/hypoxysordarin biosynthesis cluster protein G / Diels Alderase SdnG


Mass: 16300.336 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sordaria araneosa (fungus) / Gene: sdnG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B4XBH4
#2: Chemical
ChemComp-A1LYT / (5R)-5-methyl-5-[[(1R,2R,5R)-2-methyl-5-[(2R)-1-oxidanylidenepropan-2-yl]cyclopentyl]methyl]-2-propan-2-yl-cyclopenta-1,3-diene-1-carboxylic acid


Mass: 318.450 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C20H30O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 302 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.61 Å3/Da / Density % sol: 52.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02M of each alcohol, 0.1M Bicine/Tris pH 8.5, alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2- propanediol, 0.2M 2-propanol, 0.2M 1,4- ...Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02M of each alcohol, 0.1M Bicine/Tris pH 8.5, alcohol (0.2M 1,6-hexanediol, 0.2M 1-butanol, 0.2M (RS)-1,2- propanediol, 0.2M 2-propanol, 0.2M 1,4-butanediol, 0.2M 1,3-propanediol)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97852 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97852 Å / Relative weight: 1
ReflectionResolution: 2.2→38.52 Å / Num. obs: 51083 / % possible obs: 99.7 % / Redundancy: 6.8 % / Biso Wilson estimate: 40.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rpim(I) all: 0.105 / Net I/σ(I): 14.5
Reflection shellResolution: 2.2→2.27 Å / Rmerge(I) obs: 0.971 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4441 / CC1/2: 0.682 / Rpim(I) all: 0.603 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→30.74 Å / SU ML: 0.3001 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.526
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2397 2527 4.95 %
Rwork0.2011 48539 -
obs0.203 51066 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.79 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6460 0 0 302 6762
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036658
X-RAY DIFFRACTIONf_angle_d0.64619021
X-RAY DIFFRACTIONf_chiral_restr0.04511013
X-RAY DIFFRACTIONf_plane_restr0.00461173
X-RAY DIFFRACTIONf_dihedral_angle_d13.31042563
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.240.32761310.28082702X-RAY DIFFRACTION99.58
2.24-2.290.29691450.26322673X-RAY DIFFRACTION99.72
2.29-2.340.30161330.25982694X-RAY DIFFRACTION99.51
2.34-2.390.31931590.26172672X-RAY DIFFRACTION99.65
2.39-2.450.32241520.25592671X-RAY DIFFRACTION99.75
2.45-2.520.33481390.24392679X-RAY DIFFRACTION99.75
2.52-2.590.26181480.23182687X-RAY DIFFRACTION99.54
2.59-2.680.27391150.22652718X-RAY DIFFRACTION99.61
2.68-2.770.27671620.2292649X-RAY DIFFRACTION99.5
2.77-2.880.29971250.21952707X-RAY DIFFRACTION99.65
2.88-3.010.27981390.23312694X-RAY DIFFRACTION99.86
3.01-3.170.27791470.22272693X-RAY DIFFRACTION99.86
3.17-3.370.24611410.21672711X-RAY DIFFRACTION99.79
3.37-3.630.22821320.18782711X-RAY DIFFRACTION99.82
3.63-40.23411390.18892692X-RAY DIFFRACTION99.82
4-4.570.18761530.16432712X-RAY DIFFRACTION99.86
4.57-5.750.19641240.16392746X-RAY DIFFRACTION99.72
5.75-7.410.18581430.17482728X-RAY DIFFRACTION98.9

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