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

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Basic information

Entry
Database: PDB / ID: 8yhg
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: 1.76 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 28, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3006
Polymers32,4272
Non-polymers8734
Water4,053225
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4460 Å2
ΔGint-33 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.140, 58.990, 104.760
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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 5 through 35 or resid 38...
d_2ens_1(chain "B" and (resid 5 through 35 or resid 38...

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11GLUGLULEULEUAA5 - 355 - 35
d_12ASPASPTYRTYRAA38 - 4138 - 41
d_13GLYGLYHISHISAA43 - 9043 - 90
d_14ASNASNPROPROAA92 - 9992 - 99
d_15LYSLYSGLNGLNAA101 - 137101 - 137
d_16A1LYTA1LYTA1LYTA1LYTAC201
d_17MPDMPDMPDMPDAD202
d_21GLUGLULEULEUBB5 - 355 - 35
d_22ASPASPTYRTYRBB38 - 4138 - 41
d_23GLYGLYHISHISBB43 - 9043 - 90
d_24ASNASNPROPROBB92 - 9992 - 99
d_25LYSLYSGLNGLNBB101 - 137101 - 137
d_26A1LYTA1LYTA1LYTA1LYTBE201
d_27MPDMPDMPDMPDBF202

NCS oper: (Code: givenMatrix: (0.996603325784, -0.00100115076962, 0.0823456661453), (-0.00243429333969, -0.999847286536, 0.0173054275297), (0.0823157655113, -0.0174471001368, -0.996453568133)Vector: - ...NCS oper: (Code: given
Matrix: (0.996603325784, -0.00100115076962, 0.0823456661453), (-0.00243429333969, -0.999847286536, 0.0173054275297), (0.0823157655113, -0.0174471001368, -0.996453568133)
Vector: -2.04501178809, 8.35936359789, 52.5564603836)

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Components

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


Mass: 16213.259 Da / Num. of mol.: 2
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.: 2 / Source method: obtained synthetically / Formula: C20H30O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Feature type: SUBJECT OF INVESTIGATION / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 225 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.34 Å3/Da / Density % sol: 47.45 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion / pH: 8.5
Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02M of each 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), ...Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.02M of each 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), 0.1M Bicine/Tris pH 8.5
PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 1.76→30.05 Å / Num. obs: 30140 / % possible obs: 99.6 % / Redundancy: 12.3 % / Biso Wilson estimate: 25.17 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 24.2
Reflection shellResolution: 1.78→1.84 Å / Rmerge(I) obs: 1.209 / Num. unique obs: 2922

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
AutoProcessdata reduction
AutoProcessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→25.29 Å / SU ML: 0.2162 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0747
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2331 1443 4.79 %
Rwork0.1939 28697 -
obs0.1957 30140 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.17 Å2
Refinement stepCycle: LAST / Resolution: 1.76→25.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 62 225 2390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00622264
X-RAY DIFFRACTIONf_angle_d0.87323075
X-RAY DIFFRACTIONf_chiral_restr0.0556344
X-RAY DIFFRACTIONf_plane_restr0.0089396
X-RAY DIFFRACTIONf_dihedral_angle_d15.9488847
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.95645279524 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.820.28551450.24312874X-RAY DIFFRACTION99.15
1.82-1.90.35181570.28022859X-RAY DIFFRACTION99.31
1.9-1.980.35161360.34842452X-RAY DIFFRACTION85.27
1.98-2.090.28951380.26162792X-RAY DIFFRACTION96.16
2.09-2.220.21021370.18452920X-RAY DIFFRACTION100
2.22-2.390.25571290.21912801X-RAY DIFFRACTION94.98
2.39-2.630.22821450.19152943X-RAY DIFFRACTION100
2.63-3.010.22561420.18152948X-RAY DIFFRACTION99.97
3.01-3.790.19951450.1663005X-RAY DIFFRACTION99.87
3.79-25.290.21651690.16883103X-RAY DIFFRACTION99.7
Refinement TLS params.Method: refined / Origin x: 7.84752989677 Å / Origin y: 4.26901909632 Å / Origin z: 26.6449019387 Å
111213212223313233
T0.138761873779 Å2-0.000475833391157 Å2-0.00817813214899 Å2-0.144358718699 Å2-0.0118177251635 Å2--0.164595589612 Å2
L0.778395414261 °2-0.022592787515 °20.0719353826956 °2-1.26782485117 °2-0.466173427471 °2--1.1736556731 °2
S-0.05471018249 Å °0.0310156980958 Å °-0.0139470413444 Å °0.00722234729423 Å °-0.00460324923835 Å °-0.0783847824771 Å °-0.00741700384049 Å °-0.00735555581165 Å °-0.000110599657372 Å °
Refinement TLS groupSelection details: all

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