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- PDB-7a9g: Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Myco... -

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Basic information

Entry
Database: PDB / ID: 7a9g
TitleTruncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis with intermediate 2-acetyl-thiamine diphosphate
Components1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine binding / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression ...1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine binding / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / manganese ion binding / positive regulation of gene expression / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain ...Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / : / Transketolase signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
2-ACETYL-THIAMINE DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / PHOSPHATE ION / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsGierse, R.M. / Reddem, E. / Grooves, M.R.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)731.015.414 Netherlands
CitationJournal: Sci Rep / Year: 2022
Title: First crystal structures of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Mycobacterium tuberculosis indicate a distinct mechanism of intermediate stabilization.
Authors: Gierse, R.M. / Oerlemans, R. / Reddem, E.R. / Gawriljuk, V.O. / Alhayek, A. / Baitinger, D. / Jakobi, H. / Laber, B. / Lange, G. / Hirsch, A.K.H. / Groves, M.R.
History
DepositionSep 2, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 5, 2022Group: Derived calculations / Category: atom_type / Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
BBB: 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,39025
Polymers141,9752
Non-polymers3,41523
Water7,206400
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16500 Å2
ΔGint-21 kcal/mol
Surface area34140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.865, 126.170, 79.031
Angle α, β, γ (deg.)90.000, 106.285, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AAABBB

#1: Protein 1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxyxylulose-5-phosphate synthase / DXPS


Mass: 70987.516 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria)
Gene: dxs, Rv2682c, MTCY05A6.03c / Plasmid: pETM-11 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P9WNS3, 1-deoxy-D-xylulose-5-phosphate synthase

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Non-polymers , 8 types, 423 molecules

#2: Chemical ChemComp-HTL / 2-ACETYL-THIAMINE DIPHOSPHATE / 2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZO LIUM INNER SALT P,P'-DIOXIDE


Mass: 467.351 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H21N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / 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: 2.26 Å3/Da / Density % sol: 45.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M DL-Malic acid, MES monohydrate, Tris (MMT)-buffer, pH 5.0 + 25% PEG1500
PH range: 5.0 +

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.033213 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2017 / Details: double crystal monochromator
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033213 Å / Relative weight: 1
ReflectionResolution: 1.9→48.552 Å / Num. obs: 92339 / % possible obs: 99.39 % / Redundancy: 1.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.04858 / Rpim(I) all: 0.04858 / Net I/σ(I): 12.4
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.3653 / Mean I/σ(I) obs: 2.52 / Num. unique obs: 9196 / CC1/2: 0.779 / Rpim(I) all: 0.3653 / % possible all: 99.38

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
pointless1.11.21data reduction
Aimless0.7.4data scaling
MOLREP11.6.02phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o1x

2o1x


Resolution: 1.9→48.552 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / Cross valid method: FREE R-VALUE / ESU R: 0.116 / ESU R Free: 0.113
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1904 971 1.052 %
Rwork0.1539 91368 -
all0.154 --
obs-92339 99.348 %
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: 22.378 Å2
Baniso -1Baniso -2Baniso -3
1-0.213 Å2-0 Å2-0.301 Å2
2--1.789 Å20 Å2
3----1.559 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.552 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8125 0 220 400 8745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0138513
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178080
X-RAY DIFFRACTIONr_angle_refined_deg1.4761.63211509
X-RAY DIFFRACTIONr_angle_other_deg2.3311.57318598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.32851087
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.04420.427445
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.567151294
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0971578
X-RAY DIFFRACTIONr_chiral_restr0.0720.21068
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.029607
X-RAY DIFFRACTIONr_gen_planes_other0.0110.021803
X-RAY DIFFRACTIONr_nbd_refined0.2050.21757
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.27433
X-RAY DIFFRACTIONr_nbtor_refined0.1550.24086
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0720.23763
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1190.2428
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0310.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2570.230
X-RAY DIFFRACTIONr_nbd_other0.2730.287
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.29
X-RAY DIFFRACTIONr_mcbond_it1.6212.1714345
X-RAY DIFFRACTIONr_mcbond_other1.6152.174344
X-RAY DIFFRACTIONr_mcangle_it2.3713.2445421
X-RAY DIFFRACTIONr_mcangle_other2.3713.2455422
X-RAY DIFFRACTIONr_scbond_it2.4572.5524168
X-RAY DIFFRACTIONr_scbond_other2.4562.5524169
X-RAY DIFFRACTIONr_scangle_it3.763.6656084
X-RAY DIFFRACTIONr_scangle_other3.763.6656085
X-RAY DIFFRACTIONr_lrange_it4.92726.469219
X-RAY DIFFRACTIONr_lrange_other4.91226.3849176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.283720.246704X-RAY DIFFRACTION99.1368
1.949-2.0030.205700.2096611X-RAY DIFFRACTION99.7164
2.003-2.0610.212680.1846370X-RAY DIFFRACTION99.814
2.061-2.1240.216660.1646240X-RAY DIFFRACTION99.7469
2.124-2.1940.234630.1646030X-RAY DIFFRACTION99.6402
2.194-2.2710.236620.1585856X-RAY DIFFRACTION99.5291
2.271-2.3560.204600.1415591X-RAY DIFFRACTION99.4544
2.356-2.4530.155580.1335432X-RAY DIFFRACTION99.8363
2.453-2.5620.196550.1345219X-RAY DIFFRACTION99.7919
2.562-2.6870.2530.1374984X-RAY DIFFRACTION99.6439
2.687-2.8320.225510.1434736X-RAY DIFFRACTION99.6254
2.832-3.0040.176470.1424484X-RAY DIFFRACTION99.3858
3.004-3.2110.182450.1574184X-RAY DIFFRACTION99.2024
3.211-3.4680.194420.1553937X-RAY DIFFRACTION99.4501
3.468-3.7990.146370.1413572X-RAY DIFFRACTION99.0667
3.799-4.2460.162350.1353235X-RAY DIFFRACTION98.5831
4.246-4.9020.155300.1362851X-RAY DIFFRACTION98.3276
4.902-6.0020.21260.172417X-RAY DIFFRACTION98.4684
6.002-8.4790.233190.1681875X-RAY DIFFRACTION97.9824
8.479-48.5520.119120.1771041X-RAY DIFFRACTION96.6055

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