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- PDB-8yia: The selenomethionine contained structure of SdnG -

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Basic information

Entry
Database: PDB / ID: 8yia
TitleThe selenomethionine contained structure of SdnG
ComponentsSordarin/hypoxysordarin biosynthesis cluster protein G
KeywordsBIOSYNTHETIC PROTEIN / Diels Alderase / Norbornene / Sordarin
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 / SAD / Resolution: 1.43 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)67,07710
Polymers66,3674
Non-polymers7096
Water7,620423
1
A: Sordarin/hypoxysordarin biosynthesis cluster protein G
B: Sordarin/hypoxysordarin biosynthesis cluster protein G
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5385
Polymers33,1842
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-47 kcal/mol
Surface area15040 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)33,5385
Polymers33,1842
Non-polymers3553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-47 kcal/mol
Surface area15260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.605, 73.611, 108.773
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Sordarin/hypoxysordarin biosynthesis cluster protein G


Mass: 16591.865 Da / Num. of mol.: 4
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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 423 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.37 Å3/Da / Density % sol: 48.08 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion
Details: 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, 0.1M Bicine/Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97843 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97843 Å / Relative weight: 1
ReflectionResolution: 1.43→50 Å / Num. obs: 109071 / % possible obs: 99.2 % / Redundancy: 13.1 % / Biso Wilson estimate: 13.46 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 41.214
Reflection shellResolution: 1.43→1.45 Å / Rmerge(I) obs: 1.519 / Mean I/σ(I) obs: 4.2 / Num. unique obs: 109071 / CC1/2: 0.662

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.43→23.94 Å / SU ML: 0.1348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.6041
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2187 5251 4.97 %
Rwork0.1943 100402 -
obs0.1955 105653 96.12 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.55 Å2
Refinement stepCycle: LAST / Resolution: 1.43→23.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4342 0 71 423 4836
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00684619
X-RAY DIFFRACTIONf_angle_d1.02166248
X-RAY DIFFRACTIONf_chiral_restr0.0851693
X-RAY DIFFRACTIONf_plane_restr0.0157815
X-RAY DIFFRACTIONf_dihedral_angle_d15.21841752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.43-1.440.2809590.31581302X-RAY DIFFRACTION37.36
1.44-1.460.3031300.27472707X-RAY DIFFRACTION78.59
1.46-1.480.27061540.25383155X-RAY DIFFRACTION92.07
1.48-1.50.32981800.2383301X-RAY DIFFRACTION96.43
1.5-1.520.23851750.23293361X-RAY DIFFRACTION97.6
1.52-1.540.24511700.23893421X-RAY DIFFRACTION98.2
1.54-1.560.22831800.23293380X-RAY DIFFRACTION98.1
1.56-1.580.28052070.22713329X-RAY DIFFRACTION97.63
1.58-1.610.26341620.22543403X-RAY DIFFRACTION98.48
1.61-1.640.23231920.21043399X-RAY DIFFRACTION98.63
1.64-1.660.31471630.21343445X-RAY DIFFRACTION98.66
1.66-1.690.24491700.20763365X-RAY DIFFRACTION98.83
1.69-1.730.22091630.19913457X-RAY DIFFRACTION98.75
1.73-1.760.18351470.20413471X-RAY DIFFRACTION99.1
1.76-1.80.24561980.1983420X-RAY DIFFRACTION99.26
1.8-1.840.2242070.20173407X-RAY DIFFRACTION99.04
1.84-1.890.24371590.2013471X-RAY DIFFRACTION99.37
1.89-1.940.21132070.19513421X-RAY DIFFRACTION99.48
1.94-20.20822020.18263420X-RAY DIFFRACTION99.48
2-2.060.22072170.1883413X-RAY DIFFRACTION99.4
2.06-2.130.1911660.18643478X-RAY DIFFRACTION99.59
2.13-2.220.23031950.18053481X-RAY DIFFRACTION99.78
2.22-2.320.20041980.19033477X-RAY DIFFRACTION99.73
2.32-2.440.22571650.20033485X-RAY DIFFRACTION99.92
2.44-2.590.20521530.20233545X-RAY DIFFRACTION99.92
2.59-2.790.21141920.19583508X-RAY DIFFRACTION100
2.8-3.080.23281870.19373528X-RAY DIFFRACTION99.97
3.08-3.520.22231910.18313534X-RAY DIFFRACTION99.89
3.52-4.430.18271780.1653594X-RAY DIFFRACTION99.97
4.43-23.940.19151840.18163724X-RAY DIFFRACTION99.39

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