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- PDB-8a29: Apo 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeru... -

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Basic information

Entry
Database: PDB / ID: 8a29
TitleApo 1-deoxy-D-xylulose 5-phosphate synthase from Pseudomonas aeruginosa
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 synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / chlorophyll biosynthetic process / 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 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
1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa LESB58 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHamid, R. / Adam, S. / Lacour, A. / Monjas, L. / 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 2, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 14, 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
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
Revision 1.2Sep 20, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Feb 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)405,06046
Polymers403,3406
Non-polymers1,72040
Water37,9222105
1
A: 1-deoxy-D-xylulose-5-phosphate synthase
E: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,06216
Polymers134,4472
Non-polymers61514
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-150 kcal/mol
Surface area36770 Å2
MethodPISA
2
B: 1-deoxy-D-xylulose-5-phosphate synthase
D: 1-deoxy-D-xylulose-5-phosphate synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,91915
Polymers134,4472
Non-polymers47213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8580 Å2
ΔGint-137 kcal/mol
Surface area37050 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)135,07915
Polymers134,4472
Non-polymers63213
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_554x+1/2,-y+1/2,-z-11
Buried area9330 Å2
ΔGint-125 kcal/mol
Surface area36290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.444, 137.631, 232.082
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, 2145 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: C3H8O3
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: isolated from a natural source / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-NA / SODIUM ION


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


Mass: 40.078 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Ca
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2105 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 2.56 Å3/Da / Density % sol: 51.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: 100 mM HEPES, 12% PEG 8000, 200 mM calcium acetate

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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→48.59 Å / Num. obs: 216635 / % possible obs: 99.9 % / Redundancy: 2 % / Biso Wilson estimate: 27.27 Å2 / Rmerge(I) obs: 0.05821 / Net I/σ(I): 11.09
Reflection shellResolution: 2.2→2.279 Å / Rmerge(I) obs: 0.2943 / Num. unique obs: 18663

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Processing

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

6ouv


Resolution: 2.1→48.59 Å / SU ML: 0.2348 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.667
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2239 10811 4.99 %
Rwork0.1706 205823 -
obs0.1733 216634 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.27 Å2
Refinement stepCycle: LAST / Resolution: 2.1→48.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25528 0 80 2105 27713
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011126115
X-RAY DIFFRACTIONf_angle_d1.062235398
X-RAY DIFFRACTIONf_chiral_restr0.05463969
X-RAY DIFFRACTIONf_plane_restr0.01154665
X-RAY DIFFRACTIONf_dihedral_angle_d6.29283662
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.120.32853570.24666833X-RAY DIFFRACTION99.96
2.12-2.150.28593630.23156808X-RAY DIFFRACTION99.93
2.15-2.180.30353780.22556768X-RAY DIFFRACTION99.96
2.18-2.20.29253570.21256782X-RAY DIFFRACTION100
2.2-2.230.25143690.20516788X-RAY DIFFRACTION99.92
2.23-2.260.25943300.20546836X-RAY DIFFRACTION99.94
2.26-2.290.26683840.20246799X-RAY DIFFRACTION99.93
2.29-2.330.25763640.19256806X-RAY DIFFRACTION99.96
2.33-2.370.24193630.17926798X-RAY DIFFRACTION100
2.37-2.40.2563530.18516823X-RAY DIFFRACTION99.92
2.4-2.450.24083500.17836802X-RAY DIFFRACTION100
2.45-2.490.23543750.16786836X-RAY DIFFRACTION99.97
2.49-2.540.26443420.17326864X-RAY DIFFRACTION99.94
2.54-2.590.23723450.17676801X-RAY DIFFRACTION99.93
2.59-2.650.24283380.17316905X-RAY DIFFRACTION99.96
2.65-2.710.23133460.17396821X-RAY DIFFRACTION99.96
2.71-2.780.24763560.17346825X-RAY DIFFRACTION99.83
2.78-2.850.23453780.17256825X-RAY DIFFRACTION99.93
2.85-2.930.22673610.16646836X-RAY DIFFRACTION99.86
2.93-3.030.22493550.16436848X-RAY DIFFRACTION99.97
3.03-3.140.23373620.1646868X-RAY DIFFRACTION99.97
3.14-3.260.22683570.17096855X-RAY DIFFRACTION99.96
3.26-3.410.22633590.1676905X-RAY DIFFRACTION99.86
3.41-3.590.20113750.1546855X-RAY DIFFRACTION99.96
3.59-3.820.19133580.14536909X-RAY DIFFRACTION99.89
3.82-4.110.18673920.14816878X-RAY DIFFRACTION99.89
4.11-4.520.18753560.13456943X-RAY DIFFRACTION99.71
4.52-5.180.16853410.13916978X-RAY DIFFRACTION99.69
5.18-6.520.2243710.18017016X-RAY DIFFRACTION99.58
6.52-48.590.22283760.20617212X-RAY DIFFRACTION98.92
Refinement TLS params.Method: refined / Origin x: 29.4893788708 Å / Origin y: 10.3924736287 Å / Origin z: -92.8718211865 Å
111213212223313233
T0.212554939655 Å20.00242705492089 Å2-0.00515266088315 Å2-0.201434233454 Å20.0172452155592 Å2--0.211575491978 Å2
L0.0332788592797 °20.00202445380958 °20.0132337402228 °2--0.00145352591872 °2-0.00819124875551 °2--0.00767316588361 °2
S0.00878400381775 Å °-0.0220686696096 Å °-0.0360862162088 Å °0.00805800651564 Å °-0.00197648724092 Å °-0.000767851057661 Å °0.00825965753335 Å °-0.00466370085741 Å °-0.00687455222623 Å °
Refinement TLS groupSelection details: all

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