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- PDB-4fjq: Crystal Structure of an alpha-Bisabolol synthase -

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Basic information

Entry
Database: PDB / ID: 4fjq
TitleCrystal Structure of an alpha-Bisabolol synthase
ComponentsAmorpha-4,11-diene synthase
KeywordsLYASE / sesquiterpene synthase
Function / homology
Function and homology information


amorpha-4,11-diene synthase / amorpha-4,11-diene synthase activity / diterpenoid biosynthetic process / magnesium ion binding
Similarity search - Function
Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase ...Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / Terpene cyclases, class 1, plant / Terpene synthase family, metal binding domain / Terpene synthase, N-terminal domain / Terpene synthase, N-terminal domain superfamily / Terpene synthase, N-terminal domain / Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid / Farnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Glycosyltransferase / Alpha/alpha barrel / Isoprenoid synthase domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Amorpha-4,11-diene synthase
Similarity search - Component
Biological speciesArtemisia annua (sweet wormwood)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.0001 Å
AuthorsJianxu, L. / Peng, Z.
CitationJournal: Biochem.J. / Year: 2013
Title: Rational engineering of plasticity residues of sesquiterpene synthases from Artemisia annua: product specificity and catalytic efficiency.
Authors: Li, J.X. / Fang, X. / Zhao, Q. / Ruan, J.X. / Yang, C.Q. / Wang, L.J. / Miller, D.J. / Faraldos, J.A. / Allemann, R.K. / Chen, X.Y. / Zhang, P.
History
DepositionJun 12, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 1, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Amorpha-4,11-diene synthase


Theoretical massNumber of molelcules
Total (without water)65,5071
Polymers65,5071
Non-polymers00
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.997, 77.326, 68.782
Angle α, β, γ (deg.)90.00, 102.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Amorpha-4,11-diene synthase


Mass: 65507.066 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Artemisia annua (sweet wormwood) / Gene: AaBOS, AMS1, KCS12 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: M4GGS0*PLUS, amorpha-4,11-diene synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 2.18 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7.8
Details: 0.1 M Hepes, 29% PEG3000, pH 7.8, vapor diffusion, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 30, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 35037 / % possible obs: 97.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.087 / Χ2: 1.205 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.70.52334091.178194.7
2.07-2.153.70.37234061.14195.5
2.15-2.253.80.2734291.197196.2
2.25-2.373.70.21634751.25196.5
2.37-2.523.80.15634961.199197.4
2.52-2.713.80.11935261.23197.9
2.71-2.993.80.09335281.271198.2
2.99-3.423.80.06835521.249198.3
3.42-4.313.70.0535871.179198.6
4.31-503.70.04136291.15198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5EAT

5eat


Resolution: 2.0001→39.22 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8572 / SU ML: 0.22 / σ(F): 0 / Phase error: 21.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2225 1905 5.66 %
Rwork0.1812 --
obs0.1835 33663 93.48 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.404 Å2 / ksol: 0.389 e/Å3
Displacement parametersBiso max: 89.71 Å2 / Biso mean: 26.9313 Å2 / Biso min: 8.67 Å2
Baniso -1Baniso -2Baniso -3
1--2.9185 Å20 Å2-0.9232 Å2
2--3.5322 Å2-0 Å2
3----0.6137 Å2
Refinement stepCycle: LAST / Resolution: 2.0001→39.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4268 0 0 279 4547
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074357
X-RAY DIFFRACTIONf_angle_d0.9985899
X-RAY DIFFRACTIONf_chiral_restr0.064659
X-RAY DIFFRACTIONf_plane_restr0.004741
X-RAY DIFFRACTIONf_dihedral_angle_d13.2621626
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0001-2.05010.26781110.20281972208382
2.0501-2.10550.2341300.19532104223487
2.1055-2.16750.26731310.1912150228188
2.1675-2.23750.24581300.18352169229990
2.2375-2.31740.24911340.18522212234692
2.3174-2.41020.23441370.17992250238794
2.4102-2.51990.28351350.19152299243494
2.5199-2.65270.24551390.192324246395
2.6527-2.81880.24131370.1862309244696
2.8188-3.03640.22141410.19072348248997
3.0364-3.34180.2431420.18512374251697
3.3418-3.8250.20571440.17182392253698
3.825-4.81780.17641460.15662403254999
4.8178-39.22790.19311480.18592452260098

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