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- PDB-8yi8: The complex structure of SdnG with product -

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Basic information

Entry
Database: PDB / ID: 8yi8
TitleThe complex structure of SdnG with product
ComponentsSordarin/hypoxysordarin biosynthesis cluster protein G
KeywordsBIOSYNTHETIC PROTEIN / Diels Alderase / Norbornene / Sordarin / product
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: 1.33 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
DepositionFeb 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4359
Polymers64,8534
Non-polymers1,5825
Water10,809600
1
A: Sordarin/hypoxysordarin biosynthesis cluster protein G
C: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3765
Polymers32,4272
Non-polymers9493
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2330 Å2
ΔGint-10 kcal/mol
Surface area13320 Å2
MethodPISA
2
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
D: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0594
Polymers32,4272
Non-polymers6332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-12 kcal/mol
Surface area13350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.870, 101.230, 121.420
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-449-

HOH

21C-414-

HOH

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Components

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


Mass: 16213.259 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: have some covalent linkage / Source: (gene. exp.) Sordaria araneosa (fungus) / Gene: sdnG / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1B4XBH4
#2: Chemical
ChemComp-A1LZH / deoxysordaricin


Mass: 316.435 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C20H28O3 / Source: (gene. exp.) Sordaria araneosa (fungus) / Production host: Escherichia coli BL21(DE3) (bacteria)
#3: Chemical ChemComp-A1LZK / (5R)-5-methyl-5-[[(1R,2R,5R)-2-methyl-5-(3-oxidanylideneprop-1-en-2-yl)cyclopentyl]methyl]-2-propan-2-yl-cyclopenta-1,3-diene-1-carboxylic acid


Mass: 316.435 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C20H28O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 2.13 Å3/Da / Density % sol: 42.22 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 0.1M MOPSO/bis-tris pH 6.5, 5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 1mM of each Alkali (10mM rubidium chloride, 10mM strontium acetate, 10mM cesium ...Details: 0.1M MOPSO/bis-tris pH 6.5, 5%(w/v) PEG 20K, 25%(w/v) 1,1,1-tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 1mM of each Alkali (10mM rubidium chloride, 10mM strontium acetate, 10mM cesium acetate, 10mM barium acetate)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 6, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 1.33→45.3 Å / Num. obs: 129094 / % possible obs: 99.8 % / Redundancy: 2 % / Biso Wilson estimate: 15.47 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.024 / Net I/σ(I): 20.5
Reflection shellResolution: 1.33→1.35 Å / Rmerge(I) obs: 0.78 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 6214 / CC1/2: 0.753 / Rpim(I) all: 0.436 / Rrim(I) all: 0.895

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→45.3 Å / SU ML: 0.1343 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.7753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 6412 4.97 %
Rwork0.1829 122628 -
obs0.1842 129040 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.16 Å2
Refinement stepCycle: LAST / Resolution: 1.33→45.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4293 0 111 600 5004
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0114661
X-RAY DIFFRACTIONf_angle_d1.39586359
X-RAY DIFFRACTIONf_chiral_restr0.1053712
X-RAY DIFFRACTIONf_plane_restr0.0137827
X-RAY DIFFRACTIONf_dihedral_angle_d15.11411828
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.33-1.350.28262130.26033927X-RAY DIFFRACTION97.18
1.35-1.360.27132050.25454035X-RAY DIFFRACTION98.77
1.36-1.380.26752140.2394009X-RAY DIFFRACTION99.08
1.38-1.390.25112090.22864097X-RAY DIFFRACTION99.79
1.39-1.410.22821960.21814029X-RAY DIFFRACTION99.88
1.41-1.430.25082210.21444042X-RAY DIFFRACTION100
1.43-1.450.24952380.21234070X-RAY DIFFRACTION99.86
1.45-1.470.23952170.20584009X-RAY DIFFRACTION99.91
1.47-1.50.23772240.21434095X-RAY DIFFRACTION99.93
1.5-1.520.2452210.20664055X-RAY DIFFRACTION99.98
1.52-1.550.26252190.20184059X-RAY DIFFRACTION99.95
1.55-1.580.21241900.19184083X-RAY DIFFRACTION99.98
1.58-1.610.24881870.18554088X-RAY DIFFRACTION99.98
1.61-1.640.20862080.18744086X-RAY DIFFRACTION100
1.64-1.680.24562190.18954059X-RAY DIFFRACTION100
1.68-1.710.21762000.18934116X-RAY DIFFRACTION100
1.71-1.760.19081800.19184107X-RAY DIFFRACTION100
1.76-1.810.2282010.19144100X-RAY DIFFRACTION99.98
1.81-1.860.19312420.18654064X-RAY DIFFRACTION100
1.86-1.920.24212150.19534056X-RAY DIFFRACTION100
1.92-1.990.19942250.18454110X-RAY DIFFRACTION100
1.99-2.070.19982090.18594089X-RAY DIFFRACTION99.98
2.07-2.160.19382190.1794085X-RAY DIFFRACTION100
2.16-2.270.21842000.18044133X-RAY DIFFRACTION100
2.27-2.420.20872200.18264115X-RAY DIFFRACTION100
2.42-2.60.21992000.19274136X-RAY DIFFRACTION100
2.6-2.870.21952300.1844124X-RAY DIFFRACTION100
2.87-3.280.21272210.18584168X-RAY DIFFRACTION99.98
3.28-4.130.17962190.16154173X-RAY DIFFRACTION100
4.13-45.30.1862500.15694309X-RAY DIFFRACTION99.85

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