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

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Basic information

Entry
Database: PDB / ID: 6lop
TitleCrystal Structure of Class IB terpene synthase bound with geranylgeraniol
ComponentsTetraprenyl-beta-curcumene synthase
KeywordsLYASE / TERPENE SYNTHASE
Function / homologyTetraprenyl-beta-curcumene synthase YtpB-like / Protein of unknown function (DUF2600) / Chem-ELX / Tetraprenyl-beta-curcumene synthase
Function and homology information
Biological speciesBacillus alcalophilus ATCC 27647 = CGMCC 1.3604 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.91 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)84,3404
Polymers83,7592
Non-polymers5812
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The gel-filtration chart is shown on Fig S3 in our previous paper, Fujihashi et al. Chem. Sci. (2018), 9, 3754-8, doi:10.1039/C8SC00289D.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-21 kcal/mol
Surface area29260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.964, 53.403, 76.349
Angle α, β, γ (deg.)94.640, 104.630, 113.450
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-ELX / (2~{E},6~{E},10~{E})-3,7,11,15-tetramethylhexadeca-2,6,10,14-tetraen-1-ol


Mass: 290.483 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H34O / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / 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: 42.94 % / Mosaicity: 0.27 °
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: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→48.01 Å / Num. obs: 52514 / % possible obs: 96.8 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 10
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.91-1.953.50.5434790.7370.3380.6495.5
8.96-47.963.60.0255160.9990.0150.02998.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6LOO

6loo


Resolution: 1.91→47.96 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.955 / SU B: 3.855 / SU ML: 0.109 / SU R Cruickshank DPI: 0.1619 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.162 / ESU R Free: 0.142
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2022 2557 4.9 %RANDOM
Rwork0.1613 ---
obs0.1633 49954 96.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.15 Å2 / Biso mean: 32.861 Å2 / Biso min: 17.89 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.43 Å20.28 Å2
2---1.34 Å20.38 Å2
3----0.26 Å2
Refinement stepCycle: final / Resolution: 1.91→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5765 0 42 521 6328
Biso mean--65.51 46.1 -
Num. residues----694
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0136022
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175455
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.6528156
X-RAY DIFFRACTIONr_angle_other_deg1.2711.58812681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285704
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.24723.048351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.142151049
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5221533
X-RAY DIFFRACTIONr_chiral_restr0.0680.2738
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026730
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021309
LS refinement shellResolution: 1.91→1.96 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.294 174 -
Rwork0.253 3653 -
all-3827 -
obs--95.32 %

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