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

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Basic information

Entry
Database: PDB / ID: 3sdu
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 cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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 ...Glycosyltransferase - #160 / Terpene cyclases, class 1, plant / Terpene synthase, N-terminal domain / Terpene synthase, metal-binding domain / 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
GERANYL S-THIOLODIPHOSPHATE / Alpha-bisabolene synthase
Similarity search - Component
Biological speciesAbies grandis (grand fir)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacementSAD / Resolution: 1.89 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)94,2946
Polymers93,8551
Non-polymers4395
Water13,187732
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)156.327, 54.994, 126.330
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: PLASMID / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: O81086, alpha-bisabolene synthase
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H20O6P2S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 732 / 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: 2.52 Å3/Da / Density % sol: 51.24 %
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: 8.2.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 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: 1.89→50 Å / Num. all: 75082 / Num. obs: 74671 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.3 % / Rsym value: 0.073 / Net I/σ(I): 20.7
Reflection shellResolution: 1.89→1.92 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.4 / Rsym value: 0.772 / % possible all: 93.4

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Processing

Software
NameVersionClassification
BOSdata collection
Auto-Rickshawphasing
RESOLVEmodel building
PHASERphasing
PHENIX(phenix.refine: dev_778)refinement
HKL-2000data reduction
HKL-2000data scaling
RESOLVEphasing
RefinementMethod to determine structure: molecular replacementSAD / Resolution: 1.89→48.339 Å / SU ML: 0.43 / σ(F): 1.35 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2000 2.68 %Random
Rwork0.167 ---
obs0.1681 74659 98.66 %-
all-75082 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.968 Å2 / ksol: 0.315 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.9163 Å20 Å2-0.1203 Å2
2--7.2329 Å20 Å2
3----4.3166 Å2
Refinement stepCycle: LAST / Resolution: 1.89→48.339 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6339 0 23 732 7094
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086558
X-RAY DIFFRACTIONf_angle_d0.9348918
X-RAY DIFFRACTIONf_dihedral_angle_d12.6732454
X-RAY DIFFRACTIONf_chiral_restr0.064976
X-RAY DIFFRACTIONf_plane_restr0.0041131
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-1.93420.34321180.27854300X-RAY DIFFRACTION83
1.9342-1.98650.27231420.22015129X-RAY DIFFRACTION98
1.9865-2.0450.24821440.19235231X-RAY DIFFRACTION100
2.045-2.1110.21281430.1735223X-RAY DIFFRACTION100
2.111-2.18640.20591450.16155245X-RAY DIFFRACTION100
2.1864-2.2740.21731430.15685198X-RAY DIFFRACTION100
2.274-2.37740.23191440.16025255X-RAY DIFFRACTION100
2.3774-2.50280.21141460.16185285X-RAY DIFFRACTION100
2.5028-2.65960.2191440.16295214X-RAY DIFFRACTION100
2.6596-2.86490.19561430.16835253X-RAY DIFFRACTION100
2.8649-3.15320.21441470.17385276X-RAY DIFFRACTION100
3.1532-3.60930.20721440.17225292X-RAY DIFFRACTION100
3.6093-4.54680.18541480.14465316X-RAY DIFFRACTION100
4.5468-48.35470.16781490.16335442X-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)
14.4740.55343.26691.5725-0.1473.4313-0.05240.4082-0.1856-0.08110.0575-0.1771-0.10690.4275-0.00790.1972-0.02380.03930.152-0.04190.151496.252826.347610.6023
22.0346-0.39460.28781.5187-0.05741.4778-0.00270.1594-0.2533-0.1146-0.0020.03970.35-0.1374-0.00280.2512-0.0628-0.00240.0901-0.05260.17357.71194.57249.2506
33.8578-3.8235-1.40014.57040.50671.5003-0.2651-0.5458-0.25150.2760.30610.22260.1690.0996-0.03640.2255-0.09610.00710.2650.0340.202251.01343.915826.8695
43.5502-0.2096-1.00330.84790.11493.4190.0536-0.02230.1394-0.0327-0.03770.11130.0553-0.3379-0.02440.1369-0.039-0.0040.1162-0.01070.153350.551420.716113.9191
53.12440.076-0.17621.72260.77331.774-0.0484-0.28750.28310.0369-0.02160.24540.0052-0.13890.05660.1280.01190.00540.0939-0.03790.157871.446231.20522.7864
61.30720.72690.38015.69021.78741.93020.1552-0.3177-0.03250.5537-0.21330.17460.3195-0.10670.0690.1985-0.04710.01580.1780.00430.127373.179117.468633.3725
71.35190.46440.1450.44640.0550.31360.0967-0.2747-0.14150.0496-0.0828-0.12130.0490.1257-0.03760.1056-0.00950.00820.1895-0.00090.12199.503527.333528.1778
80.9402-0.1889-0.41170.30.13880.46560.0234-0.53670.2490.1743-0.0096-0.0602-0.16360.23020.06360.1265-0.09920.00730.4046-0.11410.1467106.988446.172141.4306
91.90910.5841-1.00750.87880.17823.13380.059-0.7588-0.31970.3047-0.1369-0.07890.42320.13180.24750.0971-0.07810.09670.3412-0.00510.116991.508532.839650.6553
102.4377-0.7238-0.59382.9261.07153.1925-0.077-0.4934-0.47020.5471-0.00410.10740.44940.11410.07360.1453-0.041-0.0020.26640.03810.247396.767526.172233.358
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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