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

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Basic information

Entry
Database: PDB / ID: 5kcl
TitleCrystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with dimethylallyl S-thiolodiphosphate
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 / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 6, 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: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_close_contact / 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 / _pdbx_validate_close_contact.auth_comp_id_2 / _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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)94,3164
Polymers93,7922
Non-polymers5242
Water3,873215
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules

A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,6328
Polymers187,5834
Non-polymers1,0494
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area10810 Å2
ΔGint-25 kcal/mol
Surface area54640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.290, 132.970, 68.480
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ARG / Beg label comp-ID: ARG / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 11 - 421 / Label seq-ID: 6 - 416

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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
Details: Dimethylallyl S-Thiolodiphosphate / Source: (gene. exp.) Aspergillus terreus (mold) / Strain: A8-4 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / 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: 2.37 Å3/Da / Density % sol: 48.2 %
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: 0.97907 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97907 Å / Relative weight: 1
ReflectionResolution: 2.1→132.97 Å / Num. obs: 51286 / % possible obs: 98.6 % / Redundancy: 4.9 % / Rsym value: 0.077 / Net I/av σ(I): 7.236 / Net I/σ(I): 12.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.1-2.214.20.3562.1193
2.21-2.354.20.2482.9198.4
2.35-2.514.50.1794.1199.9
2.51-2.714.90.145.21100
2.71-2.975.40.0997.2199.9
2.97-3.325.60.06810.2199.9
3.32-3.835.60.06210.31100
3.83-4.75.40.0669.2199.8
4.7-6.645.40.04912199.1
6.64-48.1455.50.03616196.8

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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: 2.1→132.97 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.921 / SU B: 4.877 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.226 / ESU R Free: 0.184 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23313 2530 4.9 %RANDOM
Rwork0.19453 ---
obs0.19641 48717 98.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.783 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2--0.22 Å20 Å2
3----0.12 Å2
Refinement stepCycle: LAST / Resolution: 2.1→132.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 28 215 6544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0196514
X-RAY DIFFRACTIONr_bond_other_d0.0070.026246
X-RAY DIFFRACTIONr_angle_refined_deg1.8321.9758868
X-RAY DIFFRACTIONr_angle_other_deg1.366314394
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7295799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.61623.852283
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.312151087
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6251535
X-RAY DIFFRACTIONr_chiral_restr0.1180.2991
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217279
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021472
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_it2.7082.8983193
X-RAY DIFFRACTIONr_mcbond_other2.7052.8983192
X-RAY DIFFRACTIONr_mcangle_it3.7124.3363990
X-RAY DIFFRACTIONr_mcangle_other3.7134.3363991
X-RAY DIFFRACTIONr_scbond_it3.7283.3233321
X-RAY DIFFRACTIONr_scbond_other3.7283.3233322
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5974.8024878
X-RAY DIFFRACTIONr_long_range_B_refined6.94923.3777304
X-RAY DIFFRACTIONr_long_range_B_other6.95523.3577244
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 48548 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 198 -
Rwork0.229 3260 -
obs--91.02 %

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