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- PDB-9kao: CTP synthetase of pseudomonas aeruginosa PAO1 -

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Basic information

Entry
Database: PDB / ID: 9kao
TitleCTP synthetase of pseudomonas aeruginosa PAO1
ComponentsCTP synthase
KeywordsLIGASE / CTPS / CTP / UTP
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / ATP binding / metal ion binding / identical protein binding / cytosol
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / CTP synthase
Similarity search - Component
Biological speciesPseudomonas aeruginosa PAO1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsWang, C.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Crystal structure of CTPS from pseudomonas aeruginosa PAO1 at 3.2 Angstroms resolution
Authors: Wang, C.C.
History
DepositionOct 29, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,61313
Polymers121,5882
Non-polymers1,02511
Water00
1
A: CTP synthase
B: CTP synthase
hetero molecules

A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)245,22526
Polymers243,1764
Non-polymers2,05022
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area16020 Å2
ΔGint-242 kcal/mol
Surface area77470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.660, 143.660, 194.080
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein CTP synthase / Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTP synthetase / CTPS / UTP-- ...Cytidine 5'-triphosphate synthase / Cytidine triphosphate synthetase / CTP synthetase / CTPS / UTP--ammonia ligase


Mass: 60793.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) / Gene: pyrG, PA3637 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q9HXZ4, CTP synthase (glutamine hydrolysing)
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H8O2
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: 4.12 Å3/Da / Density % sol: 70.13 %
Crystal growTemperature: 289.15 K / Method: liquid diffusion / pH: 6.5
Details: 1.6 M Ammonium sulfate, 0.1 M MES pH 6.5,10 % (v/v) 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97983 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 13, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97983 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 32885 / % possible obs: 96.2 % / Redundancy: 1.9 % / Biso Wilson estimate: 81.31 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.083 / Net I/σ(I): 9.1
Reflection shellResolution: 3.2→3.28 Å / Rmerge(I) obs: 0.593 / Num. unique obs: 4604 / CC1/2: 0.601 / Rpim(I) all: 0.593 / Rrim(I) all: 0.839

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Processing

Software
NameVersionClassification
PHENIXdev_5480refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→35.08 Å / SU ML: 0.5175 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.651
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3077 1995 6.09 %
Rwork0.2827 30777 -
obs0.2842 32772 95.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.76 Å2
Refinement stepCycle: LAST / Resolution: 3.2→35.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8276 0 59 0 8335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328473
X-RAY DIFFRACTIONf_angle_d0.574311477
X-RAY DIFFRACTIONf_chiral_restr0.0441308
X-RAY DIFFRACTIONf_plane_restr0.0041489
X-RAY DIFFRACTIONf_dihedral_angle_d4.04271182
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.280.42831290.38781979X-RAY DIFFRACTION87.83
3.28-3.370.391440.39242232X-RAY DIFFRACTION99.66
3.37-3.470.39951450.37572239X-RAY DIFFRACTION99.58
3.47-3.580.37491450.35462230X-RAY DIFFRACTION98.79
3.58-3.710.35011440.34092218X-RAY DIFFRACTION98.42
3.71-3.860.33831430.32362215X-RAY DIFFRACTION97.76
3.86-4.030.36141400.3082166X-RAY DIFFRACTION95.57
4.03-4.240.34961440.29652208X-RAY DIFFRACTION97.15
4.24-4.510.31761400.26682166X-RAY DIFFRACTION95.09
4.51-4.860.27631400.24382160X-RAY DIFFRACTION94.38
4.86-5.340.32461400.27252140X-RAY DIFFRACTION92.83
5.34-6.110.30541390.2862162X-RAY DIFFRACTION93.61
6.11-7.690.2721470.27352239X-RAY DIFFRACTION95.21
7.69-35.080.21781550.20512423X-RAY DIFFRACTION97.36

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