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- PDB-9gby: Crystal structure of Pseudomonas aeruginosa IspD -

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Basic information

Entry
Database: PDB / ID: 9gby
TitleCrystal structure of Pseudomonas aeruginosa IspD
Components2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
KeywordsTRANSFERASE / CYTIDYLYLTRANSFERASE / ISPD / MEP / ISOPRENOID BIOSYNTHESYS
Function / homology
Function and homology information


2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway
Similarity search - Function
2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / : / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, conserved site / Cytidylyltransferase IspD/TarI / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
: / 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBorel, F. / D'Auria, L.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European CommissionEuropean Union
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2025
Title: Fragment Discovery by X-Ray Crystallographic Screening Targeting the CTP Binding Site of Pseudomonas Aeruginosa IspD.
Authors: Willocx, D. / D'Auria, L. / Walsh, D. / Scherer, H. / Alhayek, A. / Hamed, M.M. / Borel, F. / Diamanti, E. / Hirsch, A.K.H.
History
DepositionJul 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,0982
Polymers28,0591
Non-polymers391
Water3,063170
1
A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules

A: 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,1964
Polymers56,1182
Non-polymers782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area3440 Å2
ΔGint-10 kcal/mol
Surface area19860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.570, 75.370, 37.430
Angle α, β, γ (deg.)90.000, 104.799, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase / 4-diphosphocytidyl-2C-methyl-D-erythritol synthase / MEP cytidylyltransferase / MCT


Mass: 28058.889 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: ispD, PA3633 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P57707, 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 170 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.33 Å3/Da / Density % sol: 47.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.1M MES pH 6,5 26% Peg 500 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 1.5→33.17 Å / Num. obs: 38206 / % possible obs: 98.47 % / Redundancy: 5.7 % / Biso Wilson estimate: 30.71 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.03989 / Rpim(I) all: 0.01811 / Net I/σ(I): 15.01
Reflection shellResolution: 1.5→1.54 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.9433 / Mean I/σ(I) obs: 1.12 / Num. unique obs: 14438 / CC1/2: 0.697 / CC star: 0.906 / Rpim(I) all: 0.4242 / % possible all: 92.65

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→33.17 Å / SU ML: 0.1855 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 24.394
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2092 1911 5 %
Rwork0.1861 36271 -
obs0.1872 38182 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.07 Å2
Refinement stepCycle: LAST / Resolution: 1.5→33.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1745 0 1 170 1916
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061814
X-RAY DIFFRACTIONf_angle_d0.89222474
X-RAY DIFFRACTIONf_chiral_restr0.0549280
X-RAY DIFFRACTIONf_plane_restr0.0082328
X-RAY DIFFRACTIONf_dihedral_angle_d12.2781674
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.40481220.38672423X-RAY DIFFRACTION92.65
1.54-1.580.2931410.29272568X-RAY DIFFRACTION98.08
1.58-1.630.27011570.25252559X-RAY DIFFRACTION98.09
1.63-1.680.26951460.22852573X-RAY DIFFRACTION98.8
1.68-1.740.26081290.22652584X-RAY DIFFRACTION98.73
1.74-1.810.25121260.22722610X-RAY DIFFRACTION98.77
1.81-1.890.23151380.21312592X-RAY DIFFRACTION98.95
1.89-1.990.24781550.22588X-RAY DIFFRACTION98.95
1.99-2.120.21931250.20132618X-RAY DIFFRACTION99.35
2.12-2.280.22431290.19272622X-RAY DIFFRACTION99.31
2.28-2.510.26081380.1952605X-RAY DIFFRACTION99.03
2.51-2.870.22051470.20132617X-RAY DIFFRACTION99.5
2.87-3.620.21591380.18892629X-RAY DIFFRACTION99.57
3.62-33.170.15691200.1552683X-RAY DIFFRACTION98.8

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