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- PDB-8ii9: crystal structure of Hyp mutant from Hypoxylon sp. E7406B -

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Basic information

Entry
Database: PDB / ID: 8ii9
Titlecrystal structure of Hyp mutant from Hypoxylon sp. E7406B
ComponentsTerpene synthase
KeywordsTRANSFERASE / Terpene synthetase
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: 2.17 Å
AuthorsGao, J. / Liu, W.D. / Li, Q. / Han, X. / Wei, H.L. / Dai, Z.J. / Su, L.Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: to be published
Title: crystal structure of Hyp
Authors: Gao, J. / Liu, W.D. / Li, Q. / Han, X. / Wei, H.L. / Dai, Z.J. / Su, L.Q.
History
DepositionFeb 24, 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

Downloads & links

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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
Water3,711206
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 area1860 Å2
ΔGint-16 kcal/mol
Surface area28460 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 area2030 Å2
ΔGint-16 kcal/mol
Surface area27810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.848, 86.155, 102.173
Angle α, β, γ (deg.)77.490, 85.950, 87.720
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 82 or (resid 101...
21(chain B and (resid 1 through 21 or (resid 22...
31(chain C and (resid 1 through 21 or (resid 22...
41(chain D and (resid 1 through 21 or (resid 22...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11METMETALAALA(chain A and (resid 1 through 82 or (resid 101...AA1 - 821 - 82
12LYSLYSALAALA(chain A and (resid 1 through 82 or (resid 101...AA101 - 103101 - 103
13METMETPROPRO(chain A and (resid 1 through 82 or (resid 101...AA1 - 3671 - 367
14METMETPROPRO(chain A and (resid 1 through 82 or (resid 101...AA1 - 3671 - 367
15METMETPROPRO(chain A and (resid 1 through 82 or (resid 101...AA1 - 3671 - 367
16METMETPROPRO(chain A and (resid 1 through 82 or (resid 101...AA1 - 3671 - 367
21METMETGLNGLN(chain B and (resid 1 through 21 or (resid 22...BB1 - 211 - 21
22GLUGLUGLUGLU(chain B and (resid 1 through 21 or (resid 22...BB2222
23METMETPROPRO(chain B and (resid 1 through 21 or (resid 22...BB1 - 3671 - 367
24METMETPROPRO(chain B and (resid 1 through 21 or (resid 22...BB1 - 3671 - 367
25METMETPROPRO(chain B and (resid 1 through 21 or (resid 22...BB1 - 3671 - 367
26METMETPROPRO(chain B and (resid 1 through 21 or (resid 22...BB1 - 3671 - 367
31METMETGLNGLN(chain C and (resid 1 through 21 or (resid 22...CC1 - 211 - 21
32GLUGLUGLUGLU(chain C and (resid 1 through 21 or (resid 22...CC2222
33METMETPROPRO(chain C and (resid 1 through 21 or (resid 22...CC1 - 3671 - 367
34METMETPROPRO(chain C and (resid 1 through 21 or (resid 22...CC1 - 3671 - 367
35METMETPROPRO(chain C and (resid 1 through 21 or (resid 22...CC1 - 3671 - 367
36METMETPROPRO(chain C and (resid 1 through 21 or (resid 22...CC1 - 3671 - 367
41METMETGLNGLN(chain D and (resid 1 through 21 or (resid 22...DD1 - 211 - 21
42GLUGLUGLUGLU(chain D and (resid 1 through 21 or (resid 22...DD2222
43METMETLYSLYS(chain D and (resid 1 through 21 or (resid 22...DD1 - 3661 - 366
44METMETLYSLYS(chain D and (resid 1 through 21 or (resid 22...DD1 - 3661 - 366
45METMETLYSLYS(chain D and (resid 1 through 21 or (resid 22...DD1 - 3661 - 366
46METMETLYSLYS(chain D and (resid 1 through 21 or (resid 22...DD1 - 3661 - 366

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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.: 206 / 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: 47.82 %
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: BESSY / Beamline: 14.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.17→72.31 Å / Num. obs: 78953 / % possible obs: 98.1 % / Redundancy: 3.8 % / CC1/2: 0.78 / Net I/σ(I): 7.3
Reflection shellResolution: 2.17→2.23 Å / Num. unique obs: 5754 / CC1/2: 0.61

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlphaFold

Resolution: 2.17→34.79 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 2.06 / Phase error: 33.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2631 3924 4.98 %
Rwork0.2237 74849 -
obs0.2257 78773 97.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.72 Å2 / Biso mean: 57.7706 Å2 / Biso min: 26.48 Å2
Refinement stepCycle: final / Resolution: 2.17→34.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10258 0 0 206 10464
Biso mean---51.47 -
Num. residues----1301
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3928X-RAY DIFFRACTION10.909TORSIONAL
12B3928X-RAY DIFFRACTION10.909TORSIONAL
13C3928X-RAY DIFFRACTION10.909TORSIONAL
14D3928X-RAY DIFFRACTION10.909TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.17-2.250.42373860.40077340772696
2.25-2.340.36183970.34627429782697
2.34-2.440.3443780.30437463784197
2.44-2.570.34164070.28067485789298
2.57-2.730.35433830.28117515789898
2.73-2.940.29973920.25077455784798
2.94-3.240.31284000.2527505790598
3.24-3.710.25483950.21447539793498
3.71-4.670.21264000.17747572797299
4.67-34.790.19643860.1747546793298

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