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- PDB-8yhm: The structure of SdnG covalently binding with the cope rearrangem... -

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Basic information

Entry
Database: PDB / ID: 8yhm
TitleThe structure of SdnG covalently binding with the cope rearrangement product
ComponentsSordarin/hypoxysordarin biosynthesis cluster protein G
KeywordsBIOSYNTHETIC PROTEIN / Diels Alderase / Norbornene / Sordarin / cope rearrangement
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: 1.72 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

Downloads & links

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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
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2760 Å2
ΔGint-27 kcal/mol
Surface area12640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.830, 59.310, 107.740
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 20 or resid 22...
d_2ens_1(chain "B" and (resid 5 through 20 or resid 22...

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_11GLUGLUPHEPHEAA5 - 205 - 20
d_12VALVALLEULEUAA22 - 3522 - 35
d_13LEULEUTYRTYRAA39 - 4139 - 41
d_14GLYGLYTHRTHRAA43 - 4843 - 48
d_15GLYGLYALAALAAA50 - 9350 - 93
d_16LEULEUTYRTYRAA95 - 12695 - 126
d_17LYSLYSLYSLYSAA127127
d_18ASPASPASPASPAA128128
d_19LEULEUHISHISAA130 - 136130 - 136
d_110MPDMPDMPDMPDAC201
d_21GLUGLUPHEPHEBB5 - 205 - 20
d_22VALVALLEULEUBB22 - 3522 - 35
d_23LEULEUTYRTYRBB39 - 4139 - 41
d_24GLYGLYTHRTHRBB43 - 4843 - 48
d_25GLYGLYALAALABB50 - 9350 - 93
d_26LEULEUTYRTYRBB95 - 12695 - 126
d_27LYSLYSLYSLYSBB127127
d_28ASPASPASPASPBB128128
d_29LEULEUHISHISBB130 - 136130 - 136
d_210MPDMPDMPDMPDBE201

NCS oper: (Code: givenMatrix: (0.950287023279, 0.00872004348454, -0.311253167421), (0.0082971555276, -0.999961979151, -0.00268280872449), (-0.31126472752, -3.30776217334E-5, -0.950323244116)Vector: - ...NCS oper: (Code: given
Matrix: (0.950287023279, 0.00872004348454, -0.311253167421), (0.0082971555276, -0.999961979151, -0.00268280872449), (-0.31126472752, -3.30776217334E-5, -0.950323244116)
Vector: -9.57357976587, 9.24437814005, -59.4575050268)

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Components

#1: Protein Sordarin/hypoxysordarin biosynthesis cluster protein G


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-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Chemical ChemComp-A1LZG / (3aR,5R,5aR,8R,8aR,9aR)-5-methanoyl-8,9a-dimethyl-2-propan-2-yl-3,3a,4,5,5a,6,7,8,8a,9-decahydrocyclopenta[g]azulene-1-carboxylic acid


Mass: 318.450 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H30O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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: 2.11 Å3/Da / Density % sol: 41.84 %
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) 1,1,1tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 0.5mM of each Lanthanide: 5mM erbium(III) chloride hexahydrate, 5mM terbium(III) ...Details: 0.1M MOPSO/bis-tris pH 6.5, 5%(w/v) PEG 20K, 25% (w/v) 1,1,1tris(hydroxymethyl)propane, 1%(w/v) NDSB 195, 0.5mM of each Lanthanide: 5mM erbium(III) chloride hexahydrate, 5mM terbium(III) chloride hexahydrate, 5mM ytterbium(III) chloride hexahydrate, 5mM yttrium(III) chloride hexahydrate

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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 PILATUS3 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: 1.72→39.88 Å / Num. obs: 31340 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 25.11 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 18.9
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 1.35 / Num. unique obs: 1631 / CC1/2: 0.803

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→39.88 Å / SU ML: 0.224 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.196
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2158 1557 4.98 %
Rwork0.1902 29720 -
obs0.1914 31277 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.98 Å2
Refinement stepCycle: LAST / Resolution: 1.72→39.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1910 0 230 208 2348
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00332285
X-RAY DIFFRACTIONf_angle_d0.72973119
X-RAY DIFFRACTIONf_chiral_restr0.0556350
X-RAY DIFFRACTIONf_plane_restr0.0053408
X-RAY DIFFRACTIONf_dihedral_angle_d15.4977889
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.549243208954 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.72-1.780.26071370.25582655X-RAY DIFFRACTION99.89
1.78-1.840.31561640.27542629X-RAY DIFFRACTION99.86
1.84-1.910.36721340.2662674X-RAY DIFFRACTION99.93
1.91-20.25551360.21862648X-RAY DIFFRACTION100
2-2.110.21161470.20122671X-RAY DIFFRACTION99.96
2.11-2.240.26121360.20872695X-RAY DIFFRACTION99.93
2.24-2.410.23991460.2042671X-RAY DIFFRACTION99.89
2.41-2.650.22891450.20172709X-RAY DIFFRACTION100
2.65-3.040.2131320.19672714X-RAY DIFFRACTION100
3.04-3.820.19541520.16692746X-RAY DIFFRACTION100
3.83-4.290.16681280.16412908X-RAY DIFFRACTION99.97
Refinement TLS params.Method: refined / Origin x: -15.4577383153 Å / Origin y: 4.57463080925 Å / Origin z: -28.1365520837 Å
111213212223313233
T0.128593864104 Å2-0.00899356671786 Å20.00927097161426 Å2-0.158814524139 Å2-0.00642535024804 Å2--0.204550136766 Å2
L0.327706630868 °2-0.120962245855 °20.34349018814 °2-1.45619163974 °2-0.325853594619 °2--2.46085521109 °2
S-0.0349097438862 Å °0.014283205686 Å °-0.0253675918931 Å °0.00909815289108 Å °-0.0392668449818 Å °-0.166289301788 Å °0.00286136953696 Å °0.123112444313 Å °0.0544316092294 Å °
Refinement TLS groupSelection details: all

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