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- PDB-5kcg: Crystal structure of the aromatic prenyltransferase AtaPT (apo st... -

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Basic information

Entry
Database: PDB / ID: 5kcg
TitleCrystal structure of the aromatic prenyltransferase AtaPT (apo state) from Aspergillus terreus A8-4
Componentsaromatic prenyltransferase
KeywordsTRANSFERASE / aromatic prenyltransferase / 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 / Aromatic prenyltransferase
Function and homology information
Biological speciesAspergillus terreus (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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 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

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Assembly

Deposited unit
A: aromatic prenyltransferase
B: aromatic prenyltransferase


Theoretical massNumber of molelcules
Total (without water)93,7922
Polymers93,7922
Non-polymers00
Water4,540252
1
A: aromatic prenyltransferase
B: aromatic prenyltransferase

A: aromatic prenyltransferase
B: aromatic prenyltransferase


Theoretical massNumber of molelcules
Total (without water)187,5834
Polymers187,5834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-x+2,-y,z1
Buried area10970 Å2
ΔGint-24 kcal/mol
Surface area55120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.200, 135.810, 69.520
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) / Strain (production host): BL21(DE3) / References: UniProt: A0A1B0UHJ4*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.46 Å3/Da / Density % sol: 49.99 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1 M 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: 0.97 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.9→135.81 Å / Num. all: 71707 / Num. obs: 71707 / % possible obs: 99.1 % / Redundancy: 4.9 % / Rpim(I) all: 0.043 / Rrim(I) all: 0.098 / Rsym value: 0.088 / Net I/av σ(I): 5.417 / Net I/σ(I): 11.1 / Num. measured all: 354138
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.9-250.4161.71100
2-2.1250.2672.61100
2.12-2.274.90.1823.81100
2.27-2.454.90.13951100
2.45-2.6950.1036.6199.9
2.69-350.0739.2199.9
3-3.4750.0649.6199.4
3.47-4.254.80.0737.9199.1
4.25-6.014.70.0589.9197.9
6.01-45.344.70.04116.1179.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
MOLREPphasing
Cootmodel building
SCALA3.3.21data scaling
MOSFLMdata processing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3I4Z

3i4z


Resolution: 1.9→48.58 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.926 / SU B: 3.637 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.142 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23576 3491 4.9 %RANDOM
Rwork0.19171 ---
obs0.19384 68155 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.338 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å20 Å2
2--0.96 Å2-0 Å2
3---0.8 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6301 0 0 252 6553
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0196484
X-RAY DIFFRACTIONr_bond_other_d0.0060.026232
X-RAY DIFFRACTIONr_angle_refined_deg1.8281.9778825
X-RAY DIFFRACTIONr_angle_other_deg1.251314364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4825797
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.75823.907279
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08151088
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.4131535
X-RAY DIFFRACTIONr_chiral_restr0.1190.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0217248
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021455
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_it2.8662.7223191
X-RAY DIFFRACTIONr_mcbond_other2.8632.7213190
X-RAY DIFFRACTIONr_mcangle_it3.8544.0683987
X-RAY DIFFRACTIONr_mcangle_other3.8554.0693988
X-RAY DIFFRACTIONr_scbond_it3.9583.1943293
X-RAY DIFFRACTIONr_scbond_other3.9573.1943294
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.8084.5914839
X-RAY DIFFRACTIONr_long_range_B_refined7.2822.6057329
X-RAY DIFFRACTIONr_long_range_B_other7.25922.5417259
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23922 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 270 -
Rwork0.256 4996 -
obs--99.96 %

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