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- PDB-5kd0: Crystal structure of the aromatic prenyltransferase AtaPT(E91A) m... -

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Basic information

Entry
Database: PDB / ID: 5kd0
TitleCrystal structure of the aromatic prenyltransferase AtaPT(E91A) mutant 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 / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / GERANYL S-THIOLODIPHOSPHATE / Chem-XBU / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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 1.2Nov 8, 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 / 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)94,0385
Polymers93,0212
Non-polymers1,0173
Water1629
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules

A: aromatic prenyltransferase
B: aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,07510
Polymers186,0414
Non-polymers2,0346
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Unit cell
Length a, b, c (Å)96.690, 139.240, 68.800
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: 1 / 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: 1 / Auth seq-ID: 11 - 421 / Label seq-ID: 6 - 416

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

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.410496, -0.911852, 0.004423), (-0.911833, 0.410517, 0.006001), (-0.007288, -0.001569, -0.999972)136.298431, 87.974327, 94.421692

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Components

#1: Protein aromatic prenyltransferase


Mass: 46510.324 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.: 1 / 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 / Water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.51 Å3/Da / Density % sol: 51.03 %
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% PEG3350, 3.3% DDM

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97892 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97892 Å / Relative weight: 1
ReflectionResolution: 2.82→139.24 Å / Num. all: 22776 / Num. obs: 22776 / % possible obs: 98.8 % / Redundancy: 8.1 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.099 / Rsym value: 0.093 / Net I/av σ(I): 7.014 / Net I/σ(I): 15.8 / Num. measured all: 184329
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.82-2.977.70.3812198.4
2.97-3.157.80.272.8198.5
3.15-3.377.70.1784.3198.3
3.37-3.647.80.1295.8198.2
3.64-3.997.80.1066.8198.3
3.99-4.467.90.0768.9199.5
4.46-5.158.30.0847.6199.6
5.15-6.318.70.0698.9199.9
6.31-8.9210.20.03418.31100
8.92-56.0579.30.03215.6199.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.2data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5KCG

5kcg


Resolution: 2.82→139.24 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.866 / SU B: 16.001 / SU ML: 0.31 / Cross valid method: THROUGHOUT / ESU R Free: 0.419 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26791 1144 5 %RANDOM
Rwork0.20494 ---
obs0.20809 21593 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 41.605 Å2
Baniso -1Baniso -2Baniso -3
1-0.09 Å20 Å20 Å2
2---0 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.82→139.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6293 0 64 9 6366
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.026517
X-RAY DIFFRACTIONr_bond_other_d0.010.026260
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.9868869
X-RAY DIFFRACTIONr_angle_other_deg2.2013.00214413
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0815791
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.54523.863277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.181151079
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.4061535
X-RAY DIFFRACTIONr_chiral_restr0.090.2992
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0217238
X-RAY DIFFRACTIONr_gen_planes_other0.0070.021461
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_it2.3924.0093176
X-RAY DIFFRACTIONr_mcbond_other2.3924.0093175
X-RAY DIFFRACTIONr_mcangle_it3.8686.0113963
X-RAY DIFFRACTIONr_mcangle_other3.8686.0123964
X-RAY DIFFRACTIONr_scbond_it2.5184.3123341
X-RAY DIFFRACTIONr_scbond_other2.5184.3133342
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2186.3424907
X-RAY DIFFRACTIONr_long_range_B_refined6.4132.3237340
X-RAY DIFFRACTIONr_long_range_B_other6.4132.3267341
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCSNumber: 3686 / Type: tight thermal / Rms dev position: 4.89 Å / Weight position: 0.5
LS refinement shellResolution: 2.82→2.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.363 80 -
Rwork0.3 1570 -
obs--97.81 %

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