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- PDB-6lcd: Crystal structure of AaTPS with PPi -

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Basic information

Entry
Database: PDB / ID: 6lcd
TitleCrystal structure of AaTPS with PPi
ComponentsAaTPS
KeywordsLYASE / terpene cyclase / terpene synthase
Function / homologyFARNESYL DIPHOSPHATE
Function and homology information
Biological speciesAlternaria alternata (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AaTPS
B: AaTPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,3388
Polymers96,4772
Non-polymers8626
Water1,33374
1
A: AaTPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6945
Polymers48,2381
Non-polymers4554
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area80 Å2
ΔGint-6 kcal/mol
Surface area16780 Å2
MethodPISA
2
B: AaTPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6453
Polymers48,2381
Non-polymers4072
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-13 kcal/mol
Surface area16660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.492, 113.688, 149.915
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: Chemical ChemComp-FPP / FARNESYL DIPHOSPHATE / Farnesyl pyrophosphate


Mass: 382.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H28O7P2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.11 Å3/Da / Density % sol: 60.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: ammonium formate, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: May 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→45.747 Å / Num. obs: 33446 / % possible obs: 99 % / Redundancy: 3.6 % / Biso Wilson estimate: 59.96 Å2 / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.2
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.792 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 4408 / % possible all: 99.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
Aimlessdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LCC

6lcc


Resolution: 2.7→45.747 Å / SU ML: 0.44 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 29.75
RfactorNum. reflection% reflection
Rfree0.2826 1683 5.04 %
Rwork0.2303 --
obs0.2329 33390 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 124.49 Å2 / Biso mean: 61.1358 Å2 / Biso min: 24.59 Å2
Refinement stepCycle: final / Resolution: 2.7→45.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 22 74 5995
Biso mean--84.57 52.83 -
Num. residues----745
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.780.35561310.30432617274899
2.78-2.870.34051330.29622607274099
2.87-2.970.3541350.28862637277299
2.97-3.090.36781320.28652637276999
3.09-3.230.36651440.28152613275799
3.23-3.40.32111360.25652638277499
3.4-3.610.30321320.25052638277099
3.61-3.890.30011450.23772601274698
3.89-4.290.27111450.21192638278398
4.29-4.90.271380.19462643278198
4.91-6.180.27091480.21992681282999
6.18-45.750.2071640.19182757292197

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