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- PDB-3sdv: Structure of a three-domain sesquiterpene synthase: a prospective... -

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Basic information

Entry
Database: PDB / ID: 3sdv
TitleStructure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production
ComponentsAlpha-bisabolene synthase
KeywordsLYASE / Terpene Synthase
Function / homology
Function and homology information


alpha-bisabolene synthase / alpha-bisabolene synthase activity / diterpenoid biosynthetic process / terpene synthase activity / magnesium ion binding / cytoplasm
Similarity search - Function
Glycosyltransferase - #160 / : / 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 ...Glycosyltransferase - #160 / : / 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
(1-hydroxyethane-1,1-diyl)bis(phosphonic acid) / Alpha-bisabolene synthase
Similarity search - Component
Biological speciesAbies grandis (grand fir)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 2.2 Å
AuthorsMcAndrew, R.P. / Peralta-Yahya, P.P. / DeGiovanni, A. / Pereira, J.H. / Hadi, M.Z. / Keasling, J.D. / Adams, P.D.
CitationJournal: Structure / Year: 2011
Title: Structure of a three-domain sesquiterpene synthase: a prospective target for advanced biofuels production.
Authors: McAndrew, R.P. / Peralta-Yahya, P.P. / DeGiovanni, A. / Pereira, J.H. / Hadi, M.Z. / Keasling, J.D. / Adams, P.D.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-bisabolene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1706
Polymers93,8551
Non-polymers3145
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.771, 55.002, 127.290
Angle α, β, γ (deg.)90.00, 119.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Alpha-bisabolene synthase / (E)-alpha-bisabolene synthase / AgfEabis


Mass: 93855.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Abies grandis (grand fir) / Gene: ag1 / Plasmid: PSKB3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O81086, alpha-bisabolene synthase
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-911 / (1-hydroxyethane-1,1-diyl)bis(phosphonic acid) / Etidronic acid


Mass: 206.028 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H8O7P2 / Comment: medication, detergent*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 328 / 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: 2.55 Å3/Da / Density % sol: 51.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 100 MM TRIS, 100 MM NACL, AND 23% (W/V) PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 28, 2010
RadiationMonochromator: DOUBLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 49042 / Num. obs: 46965 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.097 / Net I/σ(I): 16.6
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.68 / Rsym value: 0.539 / % possible all: 73.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: dev_778) / Classification: refinement
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 2.2→42.355 Å / SU ML: 0.56 / σ(F): 1.35 / Phase error: 24.8 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2123 2000 4.26 %Random
Rwork0.1767 ---
obs0.1783 46940 94.76 %-
all-49042 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.975 Å2 / ksol: 0.318 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--8.8573 Å20 Å24.0764 Å2
2--16.0629 Å20 Å2
3----7.2056 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.355 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6311 0 15 328 6654
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126494
X-RAY DIFFRACTIONf_angle_d0.858830
X-RAY DIFFRACTIONf_dihedral_angle_d12.732424
X-RAY DIFFRACTIONf_chiral_restr0.06966
X-RAY DIFFRACTIONf_plane_restr0.0041116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1839-2.23850.2843930.2412103X-RAY DIFFRACTION63
2.2385-2.29910.27821200.22552697X-RAY DIFFRACTION80
2.2991-2.36670.29341340.22042996X-RAY DIFFRACTION89
2.3667-2.44310.2851410.21923181X-RAY DIFFRACTION95
2.4431-2.53040.25071500.21323355X-RAY DIFFRACTION100
2.5304-2.63170.29661500.19613372X-RAY DIFFRACTION100
2.6317-2.75150.22241500.19133372X-RAY DIFFRACTION100
2.7515-2.89650.23271510.20143386X-RAY DIFFRACTION100
2.8965-3.07790.23441480.19613358X-RAY DIFFRACTION100
3.0779-3.31550.24051520.19513381X-RAY DIFFRACTION100
3.3155-3.6490.21771510.17953406X-RAY DIFFRACTION100
3.649-4.17660.19021500.14893387X-RAY DIFFRACTION100
4.1766-5.26050.16781530.13363426X-RAY DIFFRACTION100
5.2605-42.3630.15891570.1613520X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0517-0.02264.26491.7109-0.54166.01390.06410.6543-0.1942-0.1557-0.0021-0.27590.00090.8601-0.03650.2582-0.04910.0480.3028-0.06320.266596.715925.069410.7163
23.1068-0.62990.71461.7295-0.08162.3525-0.040.2306-0.3259-0.13870.02680.05590.5248-0.2596-0.01980.4063-0.120.02340.183-0.07950.24557.9113.41549.3697
37.7252-7.0151-2.83867.3931.59392.6133-0.3898-0.7555-0.3960.50.50010.43880.33340.0514-0.10850.4194-0.1620.01190.49850.05170.294551.14782.637627.0368
46.3097-0.2397-1.65071.9274-0.05965.07890.0931-0.01640.2469-0.0201-0.0670.23620.1122-0.5536-0.01190.1996-0.0744-0.01720.2448-0.02380.204450.715319.526814.0169
54.9981-0.048-0.76132.37571.00293.4209-0.0967-0.39820.23690.0358-0.00340.3605-0.0123-0.19280.09070.17820.01340.00390.1321-0.04050.231171.538329.949123.1333
61.98090.5566-0.10798.5173.21053.16640.0946-0.4103-0.04980.6714-0.24130.29240.4154-0.06390.15620.285-0.05990.00550.26980.01450.196473.343716.258433.511
72.00870.6460.58740.56750.35040.88520.1082-0.2716-0.18740.0575-0.0475-0.16270.11270.2399-0.08090.19070.00980.00830.30990.00510.211299.716126.13128.3364
81.5906-0.30230.23780.4330.04191.14710.0024-0.71970.4340.1974-0.0169-0.1067-0.20910.29250.06030.2215-0.13110.01010.6133-0.15090.2303107.100844.955741.7477
92.44950.1138-1.63780.71310.34556.3578-0.1483-1.0473-0.42420.3356-0.03680.0380.2460.02560.18220.2364-0.1190.06970.58520.01790.301790.527432.251250.4286
103.6218-1.2707-1.0614.66131.34524.7852-0.1392-0.7351-0.58280.72350.00240.06940.58060.32510.13220.2109-0.0516-0.02250.42720.06020.355396.988924.922433.5177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 36:73)
2X-RAY DIFFRACTION2(chain A and resid 74:195)
3X-RAY DIFFRACTION3(chain A and resid 196:223)
4X-RAY DIFFRACTION4(chain A and resid 224:293)
5X-RAY DIFFRACTION5(chain A and resid 294:382)
6X-RAY DIFFRACTION6(chain A and resid 383:445)
7X-RAY DIFFRACTION7(chain A and resid 446:580)
8X-RAY DIFFRACTION8(chain A and resid 581:702)
9X-RAY DIFFRACTION9(chain A and resid 703:770)
10X-RAY DIFFRACTION10(chain A and resid 771:817)

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