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

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Basic information

Entry
Database: PDB / ID: 5kcy
TitleCrystal structure of the aromatic prenyltransferase AtaPT from Aspergillus terreus A8-4 in complex with geranyl 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 / GERANYL S-THIOLODIPHOSPHATE / Chem-XBU / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.2Mar 20, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)95,1656
Polymers93,7922
Non-polymers1,3734
Water1,45981
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules

A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)190,32912
Polymers187,5834
Non-polymers2,7468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area13140 Å2
ΔGint-31 kcal/mol
Surface area54830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.950, 134.910, 68.690
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
Source: (gene. exp.) Aspergillus terreus (mold) / Strain: A8-4 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1B0UHJ4*PLUS
#2: Chemical ChemComp-XBU / methyl (2~{R})-3-(4-hydroxyphenyl)-2-[(4-hydroxyphenyl)methyl]-4-oxidanyl-5-oxidanylidene-furan-2-carboxylate


Mass: 356.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16O7
#3: Chemical ChemComp-GST / GERANYL S-THIOLODIPHOSPHATE / S-[(2E)-3,7-DIMETHYLOCTA-2,6-DIENYL] TRIHYDROGEN THIODIPHOSPHATE


Mass: 330.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H20O6P2S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25 mM Bis-Tris, 0.2 M (NH4)2SO4, 17% PEG3350, 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: 2.3→134.91 Å / Num. all: 39454 / Num. obs: 39454 / % possible obs: 97 % / Redundancy: 3.7 % / Rpim(I) all: 0.047 / Rrim(I) all: 0.096 / Rsym value: 0.083 / Net I/av σ(I): 5.489 / Net I/σ(I): 10 / Num. measured all: 145923
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.3-2.423.20.2882.6193.2
2.42-2.573.30.2082.8196.7
2.57-2.753.60.1574.6198.4
2.75-2.973.90.1186198.8
2.97-3.2540.0943.4198.9
3.25-3.6440.0748.3198.2
3.64-4.240.0728.2197.3
4.2-5.143.80.0737.8196.6
5.14-7.273.80.0727.6196.5
7.27-55.3713.90.05310.1194.1

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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 / Resolution: 2.3→56.371 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.918 / SU B: 7.189 / SU ML: 0.173 / Cross valid method: THROUGHOUT / ESU R: 0.342 / ESU R Free: 0.237 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2456 1950 4.9 %RANDOM
Rwork0.20399 ---
obs0.20604 37460 96.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.09 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--1.16 Å20 Å2
3----1.17 Å2
Refinement stepCycle: LAST / Resolution: 2.3→56.371 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6082 0 90 81 6253
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.026325
X-RAY DIFFRACTIONr_bond_other_d0.0060.026075
X-RAY DIFFRACTIONr_angle_refined_deg1.8431.998607
X-RAY DIFFRACTIONr_angle_other_deg1.3723.00313982
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3845760
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.34824.067268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.305151052
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.7611531
X-RAY DIFFRACTIONr_chiral_restr0.1070.2965
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0216995
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021414
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_it3.3353.5873058
X-RAY DIFFRACTIONr_mcbond_other3.3363.5873057
X-RAY DIFFRACTIONr_mcangle_it5.055.3723812
X-RAY DIFFRACTIONr_mcangle_other5.0495.3723813
X-RAY DIFFRACTIONr_scbond_it3.9274.0843267
X-RAY DIFFRACTIONr_scbond_other3.9274.0843268
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2285.9044796
X-RAY DIFFRACTIONr_long_range_B_refined8.11528.5856882
X-RAY DIFFRACTIONr_long_range_B_other8.11728.5956868
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 46060 / 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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.321 117 -
Rwork0.259 2600 -
obs--91.7 %

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