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- PDB-6loo: Crystal Structure of Class IB terpene synthase bound with geranyl... -

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Basic information

Entry
Database: PDB / ID: 6loo
TitleCrystal Structure of Class IB terpene synthase bound with geranylcitronellyl diphosphate
ComponentsTetraprenyl-beta-curcumene synthase
KeywordsLYASE / TERPENE SYNTHASE
Function / homologyTetraprenyl-beta-curcumene synthase YtpB-like / Protein of unknown function (DUF2600) / Chem-ELR / Chem-ELU / Tetraprenyl-beta-curcumene synthase
Function and homology information
Biological speciesBacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsFujihashi, M. / Inagi, H. / Miki, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)17H05439 Japan
Japan Society for the Promotion of Science (JSPS)19H04652 Japan
CitationJournal: Acs Chem.Biol. / Year: 2020
Title: Characterization of Class IB Terpene Synthase: The First Crystal Structure Bound with a Substrate Surrogate.
Authors: Stepanova, R. / Inagi, H. / Sugawara, K. / Asada, K. / Nishi, T. / Ueda, D. / Yasuno, Y. / Shinada, T. / Miki, K. / Fujihashi, M. / Sato, T.
History
DepositionJan 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Tetraprenyl-beta-curcumene synthase
B: Tetraprenyl-beta-curcumene synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,1175
Polymers83,7592
Non-polymers1,3573
Water6,539363
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Gel-filtration chart can be seen on Fig. S3 on Fujihashi, M. et al (2018), 9, 3754-8, doi: 10.1039/C8SC00289D
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1740 Å2
ΔGint-22 kcal/mol
Surface area29300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.870, 53.480, 76.540
Angle α, β, γ (deg.)94.630, 104.720, 113.330
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tetraprenyl-beta-curcumene synthase / beta-C25/C30/C35-prene synthase


Mass: 41879.664 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria)
Gene: BALCAV_0202405 / Plasmid: pColdII / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: A0A094YZ24
#2: Chemical ChemComp-ELR / phosphono [(3~{S},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate


Mass: 452.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ELU / phosphono [(3~{R},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-6,10,14-trienyl] hydrogen phosphate


Mass: 452.459 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H38O7P2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.3
Details: PEG3350, Ammonium Acetate, Magnesium Chloride, Methanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→48.12 Å / Num. obs: 47141 / % possible obs: 97.8 % / Redundancy: 3.905 % / Biso Wilson estimate: 34.108 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.11 / Χ2: 0.983 / Net I/σ(I): 13.65 / Num. measured all: 184069 / Scaling rejects: 73
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.99-2.043.930.842213682360434810.5320.97896.6
2.04-2.13.9230.6312.7513115346333430.6950.73296.5
2.1-2.163.9410.5643.1812734333532310.7660.65396.9
2.16-2.223.9410.4524.0512746332232340.8580.52397.4
2.22-2.33.9230.4174.6412247321331220.8860.48397.2
2.3-2.383.9360.3515.4711626303629540.9350.40697.3
2.38-2.473.9360.2856.511394296028950.9480.3397.8
2.47-2.573.9340.2447.6310972285727890.9670.28397.6
2.57-2.683.9290.1810.0610643276727090.9810.20997.9
2.68-2.813.9290.14611.8610077261225650.9860.1798.2
2.81-2.973.920.12513.599585248524450.990.14498.4
2.97-3.153.9150.09616.399098237023240.9930.11198.1
3.15-3.363.9150.06722.018574222021900.9950.07898.6
3.36-3.633.8830.04827.537852205220220.9980.05598.5
3.63-3.983.8580.03833.787125186418470.9980.04499.1
3.98-4.453.8410.03237.136615173217220.9990.03799.4
4.45-5.143.8170.02740.425649149614800.9990.03298.9
5.14-6.293.7990.02937.24870128912820.9990.03499.5
6.29-8.93.6940.02642.1236099819770.9990.0399.6
8.9-48.123.5090.02448.1218565395290.9980.02898.1

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Processing

Software
NameVersionClassification
XSCALEdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5yo8

5yo8


Resolution: 1.99→48.12 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.941 / SU B: 5.473 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2116 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.212 / ESU R Free: 0.173
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2246 2339 5 %RANDOM
Rwork0.179 ---
obs0.1813 44802 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.86 Å2 / Biso mean: 32.585 Å2 / Biso min: 17.24 Å2
Baniso -1Baniso -2Baniso -3
1-1.49 Å20.76 Å2-0.11 Å2
2---0.93 Å20.28 Å2
3----0.78 Å2
Refinement stepCycle: final / Resolution: 1.99→48.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5767 0 116 363 6246
Biso mean--74.64 38.72 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0136230
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175644
X-RAY DIFFRACTIONr_angle_refined_deg1.321.6688457
X-RAY DIFFRACTIONr_angle_other_deg1.2811.60713140
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6635730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.35523.175359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.514151082
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.0321533
X-RAY DIFFRACTIONr_chiral_restr0.0720.2757
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026966
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021341
LS refinement shellResolution: 1.99→2.042 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 193 -
Rwork0.283 3279 -
all-3472 -
obs--96.39 %

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