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- PDB-8a4d: 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aerugino... -

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Basic information

Entry
Database: PDB / ID: 8a4d
Title1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa with a thiamine analog inhibitor
Components1-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 biosynthetic process / 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
Chem-26G / 1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / pdbx_validate_planes
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_validate_planes.type
Revision 1.2Sep 6, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.4Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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)405,35531
Polymers403,3406
Non-polymers2,01425
Water37,8862103
1
A: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0529
Polymers134,4472
Non-polymers6067
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8230 Å2
ΔGint-97 kcal/mol
Surface area36780 Å2
MethodPISA
2
B: 1-deoxy-D-xylulose-5-phosphate synthase
E: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,0468
Polymers134,4472
Non-polymers6006
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-76 kcal/mol
Surface area36780 Å2
MethodPISA
3
F: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules

C: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,25614
Polymers134,4472
Non-polymers80912
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area8780 Å2
ΔGint-116 kcal/mol
Surface area36380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.618, 137.618, 231.681
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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)
Strain: LESB58 / 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 , 6 types, 2128 molecules

#2: Chemical
ChemComp-26G / 2-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]phenyl}ethanol


Mass: 243.304 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C14H17N3O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2103 / 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: 2.5 Å3/Da / Density % sol: 50.87 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
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: X06DA / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 27, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.1→48.71 Å / Num. obs: 216634 / % possible obs: 99.63 % / Redundancy: 2 % / Biso Wilson estimate: 25.24 Å2 / Rmerge(I) obs: 0.1092 / Net I/σ(I): 6.86
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.5661 / Num. unique obs: 18546

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Processing

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

6ouv


Resolution: 2.2→48.54 Å / SU ML: 0.2667 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2409 9351 4.97 %
Rwork0.1758 178782 -
obs0.179 188257 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.56 Å2
Refinement stepCycle: LAST / Resolution: 2.2→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25673 0 132 2103 27908
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011526316
X-RAY DIFFRACTIONf_angle_d1.121435675
X-RAY DIFFRACTIONf_chiral_restr0.06333984
X-RAY DIFFRACTIONf_plane_restr0.01154701
X-RAY DIFFRACTIONf_dihedral_angle_d6.95113688
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.220.32313160.24975900X-RAY DIFFRACTION99.9
2.22-2.250.34242990.27195873X-RAY DIFFRACTION99.56
2.25-2.280.32923130.25385820X-RAY DIFFRACTION98.05
2.28-2.310.2923110.23345824X-RAY DIFFRACTION98.92
2.31-2.340.28143160.21345930X-RAY DIFFRACTION99.79
2.34-2.370.27623030.20645924X-RAY DIFFRACTION99.81
2.37-2.40.29143250.20995895X-RAY DIFFRACTION99.87
2.4-2.440.25543130.19855950X-RAY DIFFRACTION99.9
2.44-2.480.27853170.19865894X-RAY DIFFRACTION99.94
2.48-2.520.27923280.2025908X-RAY DIFFRACTION99.9
2.52-2.560.26962870.19765933X-RAY DIFFRACTION99.92
2.56-2.610.27543330.19055926X-RAY DIFFRACTION99.94
2.61-2.660.26443100.18645958X-RAY DIFFRACTION99.97
2.66-2.710.27263220.18085946X-RAY DIFFRACTION99.95
2.71-2.770.2713310.18085923X-RAY DIFFRACTION99.9
2.77-2.840.27513090.1845946X-RAY DIFFRACTION99.92
2.84-2.910.25892730.18115996X-RAY DIFFRACTION99.94
2.91-2.990.25153270.17695945X-RAY DIFFRACTION99.92
2.99-3.070.23892770.18245993X-RAY DIFFRACTION100
3.07-3.170.27083160.18165970X-RAY DIFFRACTION99.95
3.17-3.290.24763280.1755953X-RAY DIFFRACTION99.89
3.29-3.420.24183220.17025905X-RAY DIFFRACTION98.86
3.42-3.570.20872970.15285959X-RAY DIFFRACTION99.51
3.57-3.760.21283100.15046023X-RAY DIFFRACTION99.73
3.76-40.20213130.14665984X-RAY DIFFRACTION99.75
4-4.310.18293010.13196039X-RAY DIFFRACTION99.64
4.31-4.740.17923320.12716028X-RAY DIFFRACTION99.8
4.74-5.420.18862930.13836044X-RAY DIFFRACTION99.42
5.42-6.830.22953180.18336126X-RAY DIFFRACTION99.61
6.83-48.540.23493110.20126267X-RAY DIFFRACTION98.24
Refinement TLS params.Method: refined / Origin x: -29.5401759841 Å / Origin y: 10.2535292081 Å / Origin z: -23.042468879 Å
111213212223313233
T0.191760488549 Å2-0.00177286914794 Å2-0.00457594784905 Å2-0.181261287048 Å2-0.0168725899498 Å2--0.189866861491 Å2
L0.0299714893791 °2-0.00350663452091 °20.0121795285687 °2-0.00510708121944 °2-0.00259675295696 °2--0.0114050254888 °2
S0.00479981984654 Å °0.0207435910894 Å °-0.0313357379381 Å °-0.00465221806655 Å °-0.000734623844993 Å °0.0014431597363 Å °0.00848292385081 Å °0.00538385264802 Å °-0.00437278987969 Å °
Refinement TLS groupSelection details: all

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