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- PDB-6zrx: Crystal structure of 6-dimethylallyltryptophan synthase from Micr... -

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Basic information

Entry
Database: PDB / ID: 6zrx
TitleCrystal structure of 6-dimethylallyltryptophan synthase from Micromonospora olivasterospora in complex with DMASPP and Trp
ComponentsDMATS type aromatic prenyltransferase
KeywordsTRANSFERASE / Complex / ABBA-barrel fold / Prenyltransferase
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / alkaloid metabolic process / metal ion binding
Similarity search - Function
Aromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase
Similarity search - Domain/homology
Chem-6C7 / DI(HYDROXYETHYL)ETHER / TRYPTOPHAN / DMATS type aromatic prenyltransferase
Similarity search - Component
Biological speciesMicromonospora olivasterospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsOstertag, E. / Stehle, T. / Zocher, G.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)SFB -TR 261 Germany
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Reprogramming Substrate and Catalytic Promiscuity of Tryptophan Prenyltransferases.
Authors: Ostertag, E. / Zheng, L. / Broger, K. / Stehle, T. / Li, S.M. / Zocher, G.
History
DepositionJul 15, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Jan 31, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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
AAA: DMATS type aromatic prenyltransferase
BBB: DMATS type aromatic prenyltransferase
CCC: DMATS type aromatic prenyltransferase
DDD: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,57821
Polymers156,8414
Non-polymers2,73717
Water17,493971
1
AAA: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8895
Polymers39,2101
Non-polymers6794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8895
Polymers39,2101
Non-polymers6794
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
CCC: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9956
Polymers39,2101
Non-polymers7855
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
DDD: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8065
Polymers39,2101
Non-polymers5954
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.021, 98.471, 89.185
Angle α, β, γ (deg.)90.000, 107.487, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules AAABBBCCCDDD

#1: Protein
DMATS type aromatic prenyltransferase


Mass: 39210.191 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora olivasterospora (bacteria)
Gene: MolI14.36, JD77_02062 / Production host: Escherichia coli (E. coli) / References: UniProt: Q2MFY2

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Non-polymers , 5 types, 988 molecules

#2: Chemical
ChemComp-6C7 / S-(3-methylbut-2-en-1-yl) trihydrogen thiodiphosphate / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TRP / TRYPTOPHAN


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 971 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.11 Å3/Da / Density % sol: 41.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 200 mM Calcium acetate, 26% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 1.69→39.673 Å / Num. obs: 143483 / % possible obs: 98.5 % / Redundancy: 4 % / Biso Wilson estimate: 30.3 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.09 / Net I/σ(I): 11.3
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 4 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 92053 / CC1/2: 0.82 / Rrim(I) all: 0.68 / % possible all: 98.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PHASER7.1.001phasing
XSCALEdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5INJ

5inj


Resolution: 1.7→39.673 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.946 / WRfactor Rfree: 0.239 / WRfactor Rwork: 0.204 / SU B: 2.863 / SU ML: 0.093 / Average fsc free: 0.9051 / Average fsc work: 0.9139 / Cross valid method: FREE R-VALUE / ESU R: 0.129 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2302 1671 1.2 %
Rwork0.2021 137632 -
all0.202 --
obs-139303 98.729 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.708 Å2
Baniso -1Baniso -2Baniso -3
1-0.944 Å2-0 Å2-0.324 Å2
2--0.041 Å20 Å2
3----0.652 Å2
Refinement stepCycle: LAST / Resolution: 1.7→39.673 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10771 0 170 971 11912
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311550
X-RAY DIFFRACTIONr_bond_other_d0.0020.01710746
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.65215804
X-RAY DIFFRACTIONr_angle_other_deg1.2131.57424749
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.97151502
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.0219.232625
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.828151633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.90515130
X-RAY DIFFRACTIONr_chiral_restr0.0530.21436
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022622
X-RAY DIFFRACTIONr_nbd_refined0.1850.22146
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1710.210049
X-RAY DIFFRACTIONr_nbtor_refined0.1510.25542
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0740.25017
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2901
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1720.254
X-RAY DIFFRACTIONr_nbd_other0.1760.2180
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.252
X-RAY DIFFRACTIONr_mcbond_it1.1742.455909
X-RAY DIFFRACTIONr_mcbond_other1.1742.455908
X-RAY DIFFRACTIONr_mcangle_it2.0113.677420
X-RAY DIFFRACTIONr_mcangle_other2.0113.677421
X-RAY DIFFRACTIONr_scbond_it1.2032.5965641
X-RAY DIFFRACTIONr_scbond_other1.2022.5965642
X-RAY DIFFRACTIONr_scangle_it1.9823.8348376
X-RAY DIFFRACTIONr_scangle_other1.9823.8358377
X-RAY DIFFRACTIONr_lrange_it4.17329.54612784
X-RAY DIFFRACTIONr_lrange_other4.15629.48812731
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.7440.3331230.30510243X-RAY DIFFRACTION99.5869
1.744-1.7920.2711210.2739913X-RAY DIFFRACTION99.2876
1.792-1.8440.2551160.2519662X-RAY DIFFRACTION99.3295
1.844-1.90.2791130.2399302X-RAY DIFFRACTION98.2264
1.9-1.9620.2911030.2268485X-RAY DIFFRACTION92.8232
1.962-2.0310.2241070.2148798X-RAY DIFFRACTION99.5751
2.031-2.1080.2681050.2118570X-RAY DIFFRACTION99.9424
2.108-2.1930.212990.2038220X-RAY DIFFRACTION99.9159
2.193-2.2910.234970.1987955X-RAY DIFFRACTION99.9007
2.291-2.4020.243910.2017475X-RAY DIFFRACTION99.7232
2.402-2.5310.223880.1957171X-RAY DIFFRACTION99.4929
2.531-2.6840.226820.1946777X-RAY DIFFRACTION99.1758
2.684-2.8690.243770.26313X-RAY DIFFRACTION98.7635
2.869-3.0970.226720.1925917X-RAY DIFFRACTION98.8937
3.097-3.3910.183650.1895403X-RAY DIFFRACTION98.2217
3.391-3.7880.198580.1844732X-RAY DIFFRACTION94.8515
3.788-4.3670.22530.1724382X-RAY DIFFRACTION99.4841
4.367-5.3320.235460.1713722X-RAY DIFFRACTION99.3933
5.332-7.4740.199350.2272920X-RAY DIFFRACTION99.4615
7.474-39.6730.27200.2211673X-RAY DIFFRACTION98.6022

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