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- PDB-6lcc: Crystal structure of AaTPS apo -

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Basic information

Entry
Database: PDB / ID: 6lcc
TitleCrystal structure of AaTPS apo
ComponentsAaTPS
KeywordsLYASE / terpene cyclase / terpene synthase
Function / homologyFarnesyl Diphosphate Synthase / Farnesyl Diphosphate Synthase / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesAlternaria alternata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHe, H. / Mori, T. / Abe, I.
CitationJournal: Nat Commun / Year: 2020
Title: Crystal structure of AaTPS
Authors: He, H. / Mori, T. / Abe, I.
History
DepositionNov 18, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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: AaTPS
B: AaTPS


Theoretical massNumber of molelcules
Total (without water)96,4772
Polymers96,4772
Non-polymers00
Water2,450136
1
A: AaTPS


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AaTPS


Theoretical massNumber of molelcules
Total (without water)48,2381
Polymers48,2381
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.160, 115.509, 149.674
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein AaTPS


Mass: 48238.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alternaria alternata (fungus) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 3.14 Å3/Da / Density % sol: 60.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: HEPES, Ammonium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Feb 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→46.796 Å / Num. obs: 38215 / % possible obs: 100 % / Redundancy: 5.7 % / Biso Wilson estimate: 48.75 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.72 Å / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 4595 / CC1/2: 0.818

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2OA6

2oa6


Resolution: 2.6→46.796 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.24
RfactorNum. reflection% reflection
Rfree0.2367 2000 5.24 %
Rwork0.1912 --
obs0.1935 38148 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.87 Å2 / Biso mean: 48.4217 Å2 / Biso min: 20.41 Å2
Refinement stepCycle: final / Resolution: 2.6→46.796 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 0 136 6074
Biso mean---42.54 -
Num. residues----749
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.6-2.66510.33181410.25442537100
2.6651-2.73710.26891390.23242533100
2.7371-2.81760.29881430.23172575100
2.8176-2.90860.29451390.22412526100
2.9086-3.01250.29021430.22972557100
3.0125-3.13310.28511390.23732543100
3.1331-3.27570.30031420.22662555100
3.2757-3.44830.26091410.20952558100
3.4483-3.66430.26081440.19692592100
3.6643-3.94710.24341430.18512582100
3.9471-4.3440.20241420.17062581100
4.344-4.9720.21021450.162617100
4.972-6.26180.22071460.18832634100
6.2618-46.7960.17551530.1549275899

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