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- PDB-8ijt: crystal structure of Hyp N135A mutant from Hypoxylon sp. E7406B -

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Basic information

Entry
Database: PDB / ID: 8ijt
Titlecrystal structure of Hyp N135A mutant from Hypoxylon sp. E7406B
ComponentsTerpene synthase
KeywordsTRANSFERASE / Terpene synthetase / UNKNOWN FUNCTION
Function / homologyTerpene synthase family 2, C-terminal metal binding / Isoprenoid synthase domain superfamily / Terpene synthase
Function and homology information
Biological speciesHypoxylon sp. E7406B (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsGao, J. / Su, L.Q. / Li, Q. / Han, X. / Wei, H.L. / Dai, Z.J. / Liu, W.D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: crystal structure of Hyp N135A mutant from Hypoxylon sp. E7406B
Authors: Gao, J. / Su, L.Q. / Li, Q. / Han, X. / Wei, H.L. / Dai, Z.J. / Liu, W.D.
History
DepositionFeb 28, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 28, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Terpene synthase
B: Terpene synthase
C: Terpene synthase
D: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)166,6654
Polymers166,6654
Non-polymers00
Water1,27971
1
A: Terpene synthase

D: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)83,3332
Polymers83,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_564x,y+1,z-11
Buried area1990 Å2
ΔGint-15 kcal/mol
Surface area27730 Å2
MethodPISA
2
B: Terpene synthase

C: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)83,3332
Polymers83,3332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Buried area1850 Å2
ΔGint-15 kcal/mol
Surface area28260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.872, 86.230, 102.349
Angle α, β, γ (deg.)77.50, 85.91, 87.69
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Terpene synthase


Mass: 41666.305 Da / Num. of mol.: 4 / Mutation: N135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hypoxylon sp. E7406B (fungus) / Gene: Hyp3 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A023W2U8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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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: 2.36 Å3/Da / Density % sol: 47.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 13% PEG4000, 0.1 M Na3Cit, pH5.6, 0.15 M NaCl, 0.01 M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17B1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 2, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.558→58.437 Å / Num. obs: 48170 / % possible obs: 97.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.96 Å2 / CC1/2: 0.998 / Net I/σ(I): 7.8
Reflection shellResolution: 2.558→2.602 Å / Num. unique obs: 2372 / CC1/2: 0.87

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACTdata extraction
Aimlessdata scaling
PHENIXphasing
autoPROCdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.56→31.37 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 29.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2517 2398 5 %
Rwork0.2006 --
obs0.2031 47999 97.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.56→31.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10229 0 0 71 10300
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01410605
X-RAY DIFFRACTIONf_angle_d1.77814386
X-RAY DIFFRACTIONf_dihedral_angle_d7.4071402
X-RAY DIFFRACTIONf_chiral_restr0.0851599
X-RAY DIFFRACTIONf_plane_restr0.0221868
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.56-2.650.32612320.26584492X-RAY DIFFRACTION97
2.65-2.760.34562350.26114596X-RAY DIFFRACTION97
2.76-2.880.33792530.26144563X-RAY DIFFRACTION97
2.88-3.030.33622390.26814560X-RAY DIFFRACTION98
3.03-3.220.30812430.23764573X-RAY DIFFRACTION98
3.22-3.470.262370.21794545X-RAY DIFFRACTION98
3.47-3.820.25722360.19614624X-RAY DIFFRACTION98
3.82-4.370.22772510.1764528X-RAY DIFFRACTION98
4.37-5.50.2182300.17184588X-RAY DIFFRACTION98
5.51-31.370.20392420.17244532X-RAY DIFFRACTION97

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