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- PDB-8a45: Structural analysis of 1-deoxy-D-xylulose 5-phosphate synthase fr... -

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Basic information

Entry
Database: PDB / ID: 8a45
TitleStructural analysis of 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa with 2-acetyl thiamine diphosphate
Components1-deoxy-D-xylulose-5-phosphate synthase
KeywordsTRANSFERASE / Complex structure / inhibitor / paDXPS.
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / : / 1-deoxy-D-xylulose-5-phosphate synthase activity / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / thiamine pyrophosphate binding / magnesium ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase, C-terminal domain / 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 / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHamid, R. / Hirsch, A.
Funding support Germany, 1items
OrganizationGrant numberCountry
Helmholtz Association Germany
CitationJournal: J.Biol.Chem. / Year: 2023
Title: 1-deoxy-D-xylulose-5-phosphate synthase from Pseudomonas aeruginosa and Klebsiella pneumoniae reveals conformational changes upon cofactor binding.
Authors: Hamid, R. / Adam, S. / Lacour, A. / Monjas, L. / Kohnke, J. / Hirsch, A.K.H.
History
DepositionJun 10, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.accession_code / _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type
Revision 1.2Jan 17, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model / Item: _pdbx_initial_refinement_model.accession_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase
C: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
E: 1-deoxy-D-xylulose-5-phosphate synthase
F: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)406,86334
Polymers403,3406
Non-polymers3,52328
Water39,4892192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase
C: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
E: 1-deoxy-D-xylulose-5-phosphate synthase
F: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules

A: 1-deoxy-D-xylulose-5-phosphate synthase
B: 1-deoxy-D-xylulose-5-phosphate synthase
C: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
E: 1-deoxy-D-xylulose-5-phosphate synthase
F: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)813,72668
Polymers806,68112
Non-polymers7,04656
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_466x-1/2,-y+3/2,-z+11
MethodPISA
Unit cell
Length a, b, c (Å)117.120, 138.013, 231.626
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

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Protein , 1 types, 6 molecules ABCDEF

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


Mass: 67223.375 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa LESB58 (bacteria)
Gene: dxs, PLES_09321 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: B7V7R4, 1-deoxy-D-xylulose-5-phosphate synthase

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Non-polymers , 5 types, 2220 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.: 6 / Source method: obtained synthetically / Formula: C14H21N4O8P2S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: Ca
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2192 / 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: 2.44 Å3/Da / Density % sol: 49.6 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion / pH: 8
Details: 100mM HEPES, 12% PEG-8000 and 200mM calcium acetate
PH range: 7.5-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.97 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2→48.59 Å / Num. obs: 250709 / % possible obs: 99.62 % / Redundancy: 2 % / Biso Wilson estimate: 24.2 Å2 / Rmerge(I) obs: 0.03098 / Net I/σ(I): 18.01
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.1424 / Num. unique obs: 18663

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487model building
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6ouv

6ouv


Resolution: 2→48.59 Å / SU ML: 0.1938 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.8037
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2174 12516 4.99 %RANDOM
Rwork0.1828 238192 --
obs0.1845 250708 99.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.13 Å2
Refinement stepCycle: LAST / Resolution: 2→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25995 0 196 2192 28383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002426692
X-RAY DIFFRACTIONf_angle_d0.562836216
X-RAY DIFFRACTIONf_chiral_restr0.04124040
X-RAY DIFFRACTIONf_plane_restr0.00444751
X-RAY DIFFRACTIONf_dihedral_angle_d6.47593743
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.28824410.25047799X-RAY DIFFRACTION99.34
2.02-2.050.26133840.23237925X-RAY DIFFRACTION99.76
2.05-2.070.26744410.23117859X-RAY DIFFRACTION99.56
2.07-2.10.27684540.22227889X-RAY DIFFRACTION99.64
2.1-2.130.24624250.21117909X-RAY DIFFRACTION99.89
2.13-2.150.25234300.20967839X-RAY DIFFRACTION99.7
2.15-2.190.23773860.2037941X-RAY DIFFRACTION99.68
2.19-2.220.21953930.19547925X-RAY DIFFRACTION99.77
2.22-2.250.24034300.19687824X-RAY DIFFRACTION98.38
2.25-2.290.21483980.1977713X-RAY DIFFRACTION96.85
2.29-2.330.23294040.19727848X-RAY DIFFRACTION99.61
2.33-2.370.23714420.19137938X-RAY DIFFRACTION99.83
2.37-2.420.22943970.18617959X-RAY DIFFRACTION99.82
2.42-2.470.23524200.18717918X-RAY DIFFRACTION99.8
2.47-2.520.23084230.18587940X-RAY DIFFRACTION99.8
2.52-2.580.22434280.18387912X-RAY DIFFRACTION99.88
2.58-2.640.22683850.18217975X-RAY DIFFRACTION99.82
2.64-2.710.21184010.18097998X-RAY DIFFRACTION99.81
2.71-2.790.23514070.18457973X-RAY DIFFRACTION99.77
2.79-2.880.22854310.19417946X-RAY DIFFRACTION99.83
2.88-2.990.23783700.1898005X-RAY DIFFRACTION99.8
2.99-3.110.2193990.18377990X-RAY DIFFRACTION99.75
3.11-3.250.23864130.18197782X-RAY DIFFRACTION96.98
3.25-3.420.21223750.18247891X-RAY DIFFRACTION97.96
3.42-3.630.20774400.17278004X-RAY DIFFRACTION99.94
3.63-3.910.19654210.16088053X-RAY DIFFRACTION99.94
3.91-4.310.18714730.14838019X-RAY DIFFRACTION99.93
4.31-4.930.17124570.14478085X-RAY DIFFRACTION99.94
4.93-6.210.19444420.17048099X-RAY DIFFRACTION99.24
6.21-48.590.21964060.20868234X-RAY DIFFRACTION97.09
Refinement TLS params.Method: refined / Origin x: 29.5568530327 Å / Origin y: 79.0920719869 Å / Origin z: 138.821838641 Å
111213212223313233
T0.212959434941 Å2-0.00108013102533 Å2-0.01140299586 Å2-0.225293099418 Å20.021408585182 Å2--0.218781340596 Å2
L0.0282451709231 °2-0.00115559166225 °20.0101673458344 °2--0.000801590859415 °2-0.0051747114138 °2---0.00632363999374 °2
S0.0112223683794 Å °-0.0229326729612 Å °-0.0297903630686 Å °0.0104788460727 Å °-0.00212749011696 Å °-0.00365134534698 Å °0.00897791524128 Å °-0.00566317148193 Å °-0.00675761414213 Å °
Refinement TLS groupSelection details: all

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