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- PDB-5kd6: Crystal structure of the aromatic prenyltransferase AtaPT from As... -

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Basic information

Entry
Database: PDB / ID: 5kd6
TitleCrystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate and (-)-butyrolactone II
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / substrate promiscuity / ABBA fold
Function / homologyAromatic prenyltransferase DMATS-type, fungi / Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / DIMETHYLALLYL S-THIOLODIPHOSPHATE / Chem-LBU / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsSun, F. / Gao, B.
Funding support China, 3items
OrganizationGrant numberCountry
Chinese Academy of SciencesXDB08030202 China
Ministry of Science and Technology of China2014CB910700 China
National Natural Science Foundation of China81302667 China
CitationJournal: Nat. Chem. Biol. / Year: 2017
Title: Molecular insights into the enzyme promiscuity of an aromatic prenyltransferase.
Authors: Chen, R. / Gao, B. / Liu, X. / Ruan, F. / Zhang, Y. / Lou, J. / Feng, K. / Wunsch, C. / Li, S.M. / Dai, J. / Sun, F.
History
DepositionJun 7, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 5, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 2.0Oct 16, 2019Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_special_symmetry / refine_hist / struct_site
Item: _atom_site.auth_comp_id / _atom_site.label_comp_id ..._atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _refine_hist.d_res_low / _struct_site.details / _struct_site.pdbx_auth_comp_id
Revision 2.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6725
Polymers93,7922
Non-polymers8813
Water11,782654
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules

A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,34410
Polymers187,5834
Non-polymers1,7616
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)96.060, 134.140, 68.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-898-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.3285, -0.944456, 0.009537), (-0.944349, 0.328613, 0.014776), (-0.01709, -0.004152, -0.999845)127.229988, 90.12487, 93.995522

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Components

#1: Protein aromatic prenyltransferase


Mass: 46895.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus terreus (mold) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0UHJ4*PLUS
#2: Chemical ChemComp-DST / DIMETHYLALLYL S-THIOLODIPHOSPHATE / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S
#3: Chemical ChemComp-LBU / methyl (2S)-4-hydroxy-3-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-5-oxo-2,5-dihydrofuran-2-carboxylate


Mass: 356.326 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H16O7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 654 / Source method: isolated from a natural source / Formula: H2O
Source detailsThe sequence database ID is Gene Bank accession number of KP893683. The residues 6-10 are expression tags.

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25 mM Bis-Tris pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.99999 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 7, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 1.84→134.14 Å / Num. all: 77116 / Num. obs: 77116 / % possible obs: 99.4 % / Redundancy: 4.6 % / Rpim(I) all: 0.04 / Rrim(I) all: 0.088 / Rsym value: 0.077 / Net I/av σ(I): 5.651 / Net I/σ(I): 12.3 / Num. measured all: 355651
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.84-1.944.60.3662.1199.5
1.94-2.064.60.233.3199.8
2.06-2.24.70.1524.9199.7
2.2-2.384.70.1126.5199.7
2.38-2.64.70.0867.9199.7
2.6-2.914.70.06610199.7
2.91-3.364.60.0619.6199.7
3.36-4.114.50.0678.3199.6
4.11-5.824.40.0619.1197.9
5.82-45.2194.50.04811.3195.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KCG

5kcg


Resolution: 1.84→45.219 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.931 / SU B: 2.957 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.133 / ESU R Free: 0.132 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22785 3847 5 %RANDOM
Rwork0.17971 ---
obs0.1821 73216 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 26.32 Å2
Baniso -1Baniso -2Baniso -3
1--0.5 Å20 Å20 Å2
2--0.28 Å20 Å2
3---0.22 Å2
Refinement stepCycle: LAST / Resolution: 1.84→45.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6321 0 54 654 7029
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0196538
X-RAY DIFFRACTIONr_bond_other_d0.0020.026256
X-RAY DIFFRACTIONr_angle_refined_deg1.8781.988903
X-RAY DIFFRACTIONr_angle_other_deg1.0523.00114415
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4985799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46123.865282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.71151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6691535
X-RAY DIFFRACTIONr_chiral_restr0.1220.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217306
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021477
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.2132.3093196
X-RAY DIFFRACTIONr_mcbond_other2.2112.3093195
X-RAY DIFFRACTIONr_mcangle_it3.0543.4553995
X-RAY DIFFRACTIONr_mcangle_other3.0533.4553996
X-RAY DIFFRACTIONr_scbond_it3.3162.7253342
X-RAY DIFFRACTIONr_scbond_other3.3152.7263343
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0483.9174909
X-RAY DIFFRACTIONr_long_range_B_refined6.95520.2688010
X-RAY DIFFRACTIONr_long_range_B_other6.69919.7037675
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.84→1.888 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.276 282 -
Rwork0.221 5335 -
obs--99.22 %

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