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- PDB-8gy0: Agrocybe pediades linalool sunthase (Ap.LS) -

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Basic information

Entry
Database: PDB / ID: 8gy0
TitleAgrocybe pediades linalool sunthase (Ap.LS)
ComponentsTerpene synthase
KeywordsBIOSYNTHETIC PROTEIN / Monoterpene synthase
Function / homologyLyases; Carbon-oxygen lyases; Acting on phosphates / Terpene cyclase-like 2 / : / Terpene synthase family 2, C-terminal metal binding / isoprenoid biosynthetic process / Isoprenoid synthase domain superfamily / lyase activity / metal ion binding / Terpene synthase
Function and homology information
Biological speciesAgrocybe pediades (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.988 Å
AuthorsRehka, T. / Sharma, D. / Lin, F. / Lim, C. / Choong, Y.K. / Chacko, J. / Zhang, C.
Funding support Singapore, 2items
OrganizationGrant numberCountry
Other governmentA2084c0064 Singapore
Other privateASTAR Singapore
CitationJournal: Acs Catalysis / Year: 2023
Title: Structural Understanding of Fungal Terpene Synthases for the Formation of Linear or Cyclic Terpene Products.
Authors: T, R. / Sharma, D. / Lin, F. / Choong, Y.K. / Lim, C. / Jobichen, C. / Zhang, C.
History
DepositionSep 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 12, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2May 8, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Terpene synthase
A: Terpene synthase


Theoretical massNumber of molelcules
Total (without water)74,8782
Polymers74,8782
Non-polymers00
Water1,44180
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-12 kcal/mol
Surface area28240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.925, 80.665, 69.906
Angle α, β, γ (deg.)90.000, 96.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Terpene synthase


Mass: 37439.199 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrocybe pediades (fungus) / Gene: D9613_012268 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A8H4VHP2, Lyases; Carbon-oxygen lyases; Acting on phosphates
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.62 Å3/Da / Density % sol: 53.08 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 10mM MgCl2, 0.2 M Sodium citrate tribasic dihydrate pH 5.6, 2% v/v Tacsimate pH 5 and 18% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 24, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.98→50 Å / Num. obs: 48065 / % possible obs: 90.5 % / Redundancy: 5.8 % / Rsym value: 0.089 / Net I/σ(I): 29.7
Reflection shellResolution: 1.98→2.01 Å / Num. unique obs: 1368 / Rsym value: 0.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MADSYSphasing
RefinementMethod to determine structure: MAD
Starting model: 1ps1, 2wbu

1ps1

2wbu


Resolution: 1.988→46.804 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 9.291 / SU ML: 0.225 / Cross valid method: FREE R-VALUE / ESU R: 0.224 / ESU R Free: 0.206
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2745 1831 4.158 %
Rwork0.2144 42208 -
all0.217 --
obs-44039 82.681 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 66.281 Å2
Baniso -1Baniso -2Baniso -3
1-3.179 Å2-0 Å20.546 Å2
2---6.036 Å2-0 Å2
3---2.682 Å2
Refinement stepCycle: LAST / Resolution: 1.988→46.804 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5049 0 0 80 5129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0135179
X-RAY DIFFRACTIONr_bond_other_d0.0010.0154728
X-RAY DIFFRACTIONr_angle_refined_deg1.4481.6427022
X-RAY DIFFRACTIONr_angle_other_deg1.2991.5810863
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345626
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.422.381294
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.26915846
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.851532
X-RAY DIFFRACTIONr_chiral_restr0.0680.2672
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025922
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021282
X-RAY DIFFRACTIONr_nbd_refined0.2080.21259
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1980.24370
X-RAY DIFFRACTIONr_nbtor_refined0.1770.22593
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0790.22367
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.2154
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.120.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.130.216
X-RAY DIFFRACTIONr_nbd_other0.2460.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.230.24
X-RAY DIFFRACTIONr_mcbond_it6.1716.9482510
X-RAY DIFFRACTIONr_mcbond_other6.1686.9452509
X-RAY DIFFRACTIONr_mcangle_it8.68110.4013134
X-RAY DIFFRACTIONr_mcangle_other8.68210.4033135
X-RAY DIFFRACTIONr_scbond_it6.0937.2842669
X-RAY DIFFRACTIONr_scbond_other6.0927.2862670
X-RAY DIFFRACTIONr_scangle_it8.90410.7413888
X-RAY DIFFRACTIONr_scangle_other8.90310.7423889
X-RAY DIFFRACTIONr_lrange_it11.6880.4676108
X-RAY DIFFRACTIONr_lrange_other11.6980.4696096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.988-2.0390.341700.3931435X-RAY DIFFRACTION38.3635
2.039-2.0950.425800.3541850X-RAY DIFFRACTION50.3391
2.095-2.1560.379850.3282160X-RAY DIFFRACTION60.9723
2.156-2.2220.3321130.3432496X-RAY DIFFRACTION71.9526
2.222-2.2950.3331050.3242699X-RAY DIFFRACTION80.3899
2.295-2.3750.3631310.2952810X-RAY DIFFRACTION85.8686
2.375-2.4650.3561210.2712782X-RAY DIFFRACTION89.7928
2.465-2.5660.3681140.2642676X-RAY DIFFRACTION89.0805
2.566-2.6790.2941170.2362786X-RAY DIFFRACTION94.9313
2.679-2.810.3231150.2152667X-RAY DIFFRACTION96.1964
2.81-2.9620.291130.2372528X-RAY DIFFRACTION97.167
2.962-3.1410.2931060.2182483X-RAY DIFFRACTION98.4785
3.141-3.3570.2681000.2232315X-RAY DIFFRACTION98.4509
3.357-3.6260.275910.212126X-RAY DIFFRACTION97.9673
3.626-3.9710.226870.1751954X-RAY DIFFRACTION97.2831
3.971-4.4380.258810.171824X-RAY DIFFRACTION99.374
4.438-5.1210.243680.1771583X-RAY DIFFRACTION97.9241
5.121-6.2630.262600.2191379X-RAY DIFFRACTION99.3099
6.263-8.8210.242460.1731048X-RAY DIFFRACTION97.8533
8.821-46.8040.229280.2607X-RAY DIFFRACTION99.374

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