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- PDB-7a9h: Truncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Myco... -

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Basic information

Entry
Database: PDB / ID: 7a9h
TitleTruncated 1-deoxy-D-xylulose 5-phosphate synthase (DXS) from Mycobacterium tuberculosis
Components1-deoxy-D-xylulose-5-phosphate synthase,1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE
Function / homology
Function and homology information


thiamine binding / 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 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 ...thiamine binding / 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 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 signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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 signature 1. / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / 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
THIAMINE DIPHOSPHATE / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesMycobacterium tuberculosis H37Rv (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.849 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 1.1Oct 5, 2022Group: Database references / Derived calculations / Category: atom_type / citation / citation_author
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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 1.2Jan 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)134,2806
Polymers133,3812
Non-polymers8994
Water11,998666
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-89 kcal/mol
Surface area35320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.987, 76.100, 79.148
Angle α, β, γ (deg.)108.956, 106.530, 107.594
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 66690.461 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
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-TPP / THIAMINE DIPHOSPHATE / Thiamine pyrophosphate


Mass: 425.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H19N4O7P2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 666 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
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: Dec 3, 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: 1.849→43.832 Å / Num. obs: 93268 / % possible obs: 91 % / Redundancy: 1.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.0233 / Rpim(I) all: 0.0233 / Net I/σ(I): 20.99
Reflection shellResolution: 1.85→1.916 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.0852 / Mean I/σ(I) obs: 6.54 / Num. unique obs: 6412 / CC1/2: 0.979 / Rpim(I) all: 0.0852 / % possible all: 62.53

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSVERSION Mar 15, 2019 BUILT=20190315data reduction
XDSVERSION Mar 15, 2019 BUILT=20190315data scaling
MOLREP11.6.02phasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2o1x

2o1x


Resolution: 1.849→43.832 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.953 / WRfactor Rfree: 0.178 / WRfactor Rwork: 0.154 / Average fsc free: 0.9572 / Average fsc work: 0.9631 / Cross valid method: FREE R-VALUE / ESU R: 0.117 / ESU R Free: 0.105
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1736 2101 2.253 %
Rwork0.1507 91167 -
all0.151 --
obs-93268 90.85 %
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: 19.252 Å2
Baniso -1Baniso -2Baniso -3
1--0.044 Å20.233 Å2-0.22 Å2
2--0.678 Å20.079 Å2
3----0.432 Å2
Refinement stepCycle: LAST / Resolution: 1.849→43.832 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8162 0 54 666 8882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0138550
X-RAY DIFFRACTIONr_bond_other_d0.0350.0178074
X-RAY DIFFRACTIONr_angle_refined_deg1.371.63311649
X-RAY DIFFRACTIONr_angle_other_deg2.3581.57518601
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.25451134
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.32520.234470
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.088151347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6161586
X-RAY DIFFRACTIONr_chiral_restr0.0680.21090
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029868
X-RAY DIFFRACTIONr_gen_planes_other0.0090.021874
X-RAY DIFFRACTIONr_nbd_refined0.2050.21716
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2130.27221
X-RAY DIFFRACTIONr_nbtor_refined0.1520.24093
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0630.23569
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2526
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0850.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1470.216
X-RAY DIFFRACTIONr_nbd_other0.2230.269
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1690.227
X-RAY DIFFRACTIONr_mcbond_it1.3181.924406
X-RAY DIFFRACTIONr_mcbond_other1.3141.9194404
X-RAY DIFFRACTIONr_mcangle_it2.0392.8695509
X-RAY DIFFRACTIONr_mcangle_other2.0382.8695509
X-RAY DIFFRACTIONr_scbond_it1.8042.1294144
X-RAY DIFFRACTIONr_scbond_other1.8052.1314137
X-RAY DIFFRACTIONr_scangle_it2.8643.1026115
X-RAY DIFFRACTIONr_scangle_other2.8633.1026116
X-RAY DIFFRACTIONr_lrange_it4.3622.8869477
X-RAY DIFFRACTIONr_lrange_other4.3622.8869478
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.849-1.8970.2071000.1734356X-RAY DIFFRACTION58.794
1.897-1.9490.1921280.1675553X-RAY DIFFRACTION76.5427
1.949-2.0050.2241520.1646574X-RAY DIFFRACTION93.1579
2.005-2.0670.1781480.1566421X-RAY DIFFRACTION94.8045
2.067-2.1350.1751440.1426258X-RAY DIFFRACTION94.5922
2.135-2.2090.1881400.1466096X-RAY DIFFRACTION94.5565
2.209-2.2930.1571350.1375851X-RAY DIFFRACTION94.7152
2.293-2.3860.161300.1395637X-RAY DIFFRACTION94.7585
2.386-2.4920.161250.1295415X-RAY DIFFRACTION95.3857
2.492-2.6140.1971190.1415185X-RAY DIFFRACTION95.0878
2.614-2.7550.191140.1544921X-RAY DIFFRACTION94.9463
2.755-2.9220.1661080.1494684X-RAY DIFFRACTION95.3252
2.922-3.1230.1651000.1544374X-RAY DIFFRACTION95.4148
3.123-3.3730.179940.1644061X-RAY DIFFRACTION95.0801
3.373-3.6940.165880.1563805X-RAY DIFFRACTION95.6981
3.694-4.1280.169780.1413400X-RAY DIFFRACTION95.2355
4.128-4.7640.13690.132992X-RAY DIFFRACTION94.9736
4.764-5.8270.184590.1722545X-RAY DIFFRACTION95.8763
5.827-8.2110.171450.1751969X-RAY DIFFRACTION95.6315
8.211-43.8320.201250.1681070X-RAY DIFFRACTION93.2709

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