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- PDB-6zrz: Crystal structure of 5-dimethylallyl tryptophan synthase from Str... -

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Basic information

Entry
Database: PDB / ID: 6zrz
TitleCrystal structure of 5-dimethylallyl tryptophan synthase from Streptomyces coelicolor in complex with DMASPP and Trp
ComponentsDMATS type aromatic prenyltransferase
KeywordsTRANSFERASE / Complex / ABBA-barrel fold / Prenyltransferase
Function / homologyAromatic prenyltransferase, DMATS-type / Tryptophan dimethylallyltransferase / Aromatic prenyltransferase / alkaloid metabolic process / transferase activity, transferring alkyl or aryl (other than methyl) groups / Chem-6C7 / TRYPTOPHAN / DMATS type aromatic prenyltransferase
Function and homology information
Biological speciesStreptomyces coelicolor (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsOstertag, E. / Broger, K. / 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,8016
Polymers76,8692
Non-polymers9334
Water7,422412
1
AAA: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9013
Polymers38,4341
Non-polymers4662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
BBB: DMATS type aromatic prenyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9013
Polymers38,4341
Non-polymers4662
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.658, 70.147, 91.082
Angle α, β, γ (deg.)90.000, 92.722, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DMATS type aromatic prenyltransferase


Mass: 38434.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor (bacteria) / Gene: FHV93_101284 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A4R8NF71
#2: Chemical ChemComp-6C7 / S-(3-methylbut-2-en-1-yl) trihydrogen thiodiphosphate / DMASPP / DMAPP / DMADP / Dimethylallyl pyrophosphate / dimethylallyl diphosphate / isoprenyl pyrophosphate / Dimethylallyl pyrophosphate


Mass: 262.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H12O6P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-TRP / TRYPTOPHAN / Tryptophan


Type: L-peptide linking / Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 412 / Source method: isolated from a natural source / Formula: H2O
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: 1.82 Å3/Da / Density % sol: 32.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 150 mM Bis-Tris 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 1.696→45.5 Å / Num. obs: 62994 / % possible obs: 97 % / Redundancy: 4.5 % / Biso Wilson estimate: 32.8 Å2 / CC1/2: 0.99 / Rrim(I) all: 0.065 / Net I/σ(I): 15.4
Reflection shellResolution: 1.696→1.8 Å / Num. unique obs: 10011 / CC1/2: 0.59 / Rrim(I) all: 1

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Processing

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

5inj


Resolution: 1.696→45.49 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.95 / WRfactor Rfree: 0.205 / WRfactor Rwork: 0.17 / SU B: 6.555 / SU ML: 0.104 / Average fsc free: 0.8899 / Average fsc work: 0.8987 / Cross valid method: FREE R-VALUE / ESU R: 0.127 / ESU R Free: 0.119
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2189 1812 3 %
Rwork0.1811 58580 -
all0.182 --
obs-60392 96.948 %
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: 28.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.008 Å2-0 Å2-0.269 Å2
2--0.396 Å20 Å2
3----0.361 Å2
Refinement stepCycle: LAST / Resolution: 1.696→45.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5269 0 58 412 5739
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0135517
X-RAY DIFFRACTIONr_bond_other_d0.0040.0175078
X-RAY DIFFRACTIONr_angle_refined_deg1.4551.6587543
X-RAY DIFFRACTIONr_angle_other_deg1.341.57711692
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5855721
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.80519.103290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.10415771
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9211561
X-RAY DIFFRACTIONr_chiral_restr0.0680.2698
X-RAY DIFFRACTIONr_chiral_restr_other1.4630.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021251
X-RAY DIFFRACTIONr_nbd_refined0.1990.21133
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.24678
X-RAY DIFFRACTIONr_nbtor_refined0.1580.22685
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0810.22456
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1660.2390
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0610.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1790.238
X-RAY DIFFRACTIONr_nbd_other0.2170.2146
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1960.227
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.030.21
X-RAY DIFFRACTIONr_mcbond_it1.2752.3452875
X-RAY DIFFRACTIONr_mcbond_other1.2752.3452874
X-RAY DIFFRACTIONr_mcangle_it2.1553.5063596
X-RAY DIFFRACTIONr_mcangle_other2.1553.5063597
X-RAY DIFFRACTIONr_scbond_it1.5442.5792642
X-RAY DIFFRACTIONr_scbond_other1.5432.5792643
X-RAY DIFFRACTIONr_scangle_it2.483.7983946
X-RAY DIFFRACTIONr_scangle_other2.4793.7993947
X-RAY DIFFRACTIONr_lrange_it5.22828.9886165
X-RAY DIFFRACTIONr_lrange_other5.13428.556067
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.696-1.740.3361230.32639810.32745490.6910.68390.21760.315
1.74-1.7870.3181290.27841790.27945040.7920.80195.64830.26
1.787-1.8390.2881260.25840860.25943290.8390.83997.29730.232
1.839-1.8960.2831240.24239810.24342230.850.86597.20580.214
1.896-1.9580.2961170.24238070.24440900.8560.87795.94130.214
1.958-2.0260.2041160.19537350.19539840.9260.92196.66160.163
2.026-2.1030.2221100.20135540.20137870.9040.92196.7520.173
2.103-2.1880.1971080.17734880.17836680.9330.9498.03710.149
2.188-2.2850.2261020.18633200.18835200.9350.93197.21590.16
2.285-2.3970.2231010.17832410.17934170.9320.94397.80510.15
2.397-2.5260.221940.16830480.1732020.940.95198.12620.143
2.526-2.6790.233900.1729020.17230460.9330.94698.22720.147
2.679-2.8630.264840.17927310.18228570.9140.94198.52990.159
2.863-3.0910.196790.16925560.1726700.9430.95398.68910.157
3.091-3.3850.212730.16723520.16924630.9360.95498.45720.164
3.385-3.7820.19660.15721240.15822480.9480.96297.41990.161
3.782-4.3620.186580.14818930.14919770.9560.96798.68490.158
4.362-5.330.167490.14815950.14916660.9660.96998.67950.164
5.33-7.4860.244400.20912800.2113340.9390.94698.95050.228
7.486-45.490.195230.1647270.1657570.9550.96899.07530.204
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.1381-0.0048-0.14550.2987-0.15840.8514-0.00430.03380.06580.01780.0375-0.0280.0156-0.1297-0.03310.00250.0049-0.00280.08340.01290.03457.85282.889611.5942
20.3537-0.4420.2350.5654-0.28290.92140.06480.0203-0.0149-0.0686-0.05060.01410.01720.0845-0.01420.0295-0.01890.00190.0670.01640.016828.5371-24.8932.6961
300000000000000-00.0318000.031800.0318000
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA2 - 358
2X-RAY DIFFRACTION2ALLBBB1 - 358

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