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- PDB-8fv6: E coli. CTP synthase in complex with dF-dCTP -

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Basic information

Entry
Database: PDB / ID: 8fv6
TitleE coli. CTP synthase in complex with dF-dCTP
ComponentsCTP synthase
KeywordsCYTOSOLIC PROTEIN / LIGASE / Inhibitor complex / Metabolic enzyme
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / 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
Chem-GTF / MALONIC ACID / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsHolyoak, T. / McLeod, M.J. / Tran, N.
Funding support Canada, 2items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Canadian Institutes of Health Research (CIHR)114895 Canada
CitationJournal: Protein Sci. / Year: 2023
Title: A metal-dependent conformational change provides a structural basis for the inhibition of CTP synthase by gemcitabine-5'-triphosphate.
Authors: McLeod, M.J. / Tran, N. / McCluskey, G.D. / Gillis, T.D. / Bearne, S.L. / Holyoak, T.
History
DepositionJan 18, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
AAA: CTP synthase
BBB: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,1548
Polymers120,8942
Non-polymers1,2606
Water8,971498
1
AAA: CTP synthase
BBB: CTP synthase
hetero molecules

AAA: CTP synthase
BBB: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,30916
Polymers241,7884
Non-polymers2,52112
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area14040 Å2
ΔGint-125 kcal/mol
Surface area73850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.402, 108.955, 129.019
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11AAA-932-

HOH

21BBB-1050-

HOH

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Components

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


Mass: 60446.980 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: pyrG, ECS88_3048 / Plasmid: pET-15B / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: B7MLA1, CTP synthase (glutamine hydrolysing)
#2: Chemical ChemComp-MLA / MALONIC ACID / DICARBOXYLIC ACID C3 / PROPANEDIOLIC ACID / METHANEDICARBOXYLIC ACID


Mass: 104.061 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-GTF / 2'-deoxy-2',2'-difluorocytidine 5'-(tetrahydrogen triphosphate) / Gemcitabine-TRIPHOSPHATE


Mass: 503.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H14F2N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
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: 4.54 Å3/Da / Density % sol: 72.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M TRIS-Cl pH 8.0 (room temperature), 5 mM magnesium chloride, 1.15 - 1.4 M ammonium sulfate, 15 mg/mL CTPS.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.25→48.9 Å / Num. obs: 106448 / % possible obs: 100 % / Redundancy: 14.1 % / Biso Wilson estimate: 38.9 Å2 / CC1/2: 0.952 / CC star: 0.987 / Rmerge(I) obs: 0.134 / Rpim(I) all: 0.036 / Rrim(I) all: 0.139 / Net I/σ(I): 12.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.82 / Mean I/σ(I) obs: 2.06 / Num. unique obs: 10497 / CC1/2: 0.798 / CC star: 0.942 / Rpim(I) all: 0.233 / Rrim(I) all: 0.853 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→48.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / SU B: 5.404 / SU ML: 0.123 / Cross valid method: FREE R-VALUE / ESU R: 0.161 / ESU R Free: 0.143
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2099 5316 4.994 %
Rwork0.1896 101132 -
all0.191 --
obs-106448 99.905 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 46.454 Å2
Baniso -1Baniso -2Baniso -3
1-0.001 Å2-0 Å2-0 Å2
2---0.004 Å20 Å2
3---0.003 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 76 498 8908
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0138664
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178129
X-RAY DIFFRACTIONr_angle_refined_deg1.1771.64411775
X-RAY DIFFRACTIONr_angle_other_deg1.0811.57318860
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.71951098
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.02222.155464
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.065151503
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.491565
X-RAY DIFFRACTIONr_chiral_restr0.0430.21144
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029718
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021771
X-RAY DIFFRACTIONr_nbd_refined0.1660.21578
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1620.28027
X-RAY DIFFRACTIONr_nbtor_refined0.1430.24112
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.070.23790
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.2492
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0190.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1120.23
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1550.220
X-RAY DIFFRACTIONr_nbd_other0.1860.2111
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1670.243
X-RAY DIFFRACTIONr_mcbond_it1.5354.964308
X-RAY DIFFRACTIONr_mcbond_other1.5344.964307
X-RAY DIFFRACTIONr_mcangle_it2.7087.435386
X-RAY DIFFRACTIONr_mcangle_other2.7087.435387
X-RAY DIFFRACTIONr_scbond_it1.325.14356
X-RAY DIFFRACTIONr_scbond_other1.325.0994357
X-RAY DIFFRACTIONr_scangle_it2.3737.5716373
X-RAY DIFFRACTIONr_scangle_other2.3737.576374
X-RAY DIFFRACTIONr_lrange_it4.58957.1299425
X-RAY DIFFRACTIONr_lrange_other4.5157.0139305
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.3070.3293720.3117327X-RAY DIFFRACTION99.1756
2.307-2.370.2923810.2887243X-RAY DIFFRACTION99.9476
2.37-2.4390.3013700.2727016X-RAY DIFFRACTION100
2.439-2.5140.2723840.256794X-RAY DIFFRACTION99.9861
2.514-2.5960.2563720.2466622X-RAY DIFFRACTION100
2.596-2.6870.2663520.2316380X-RAY DIFFRACTION100
2.687-2.7890.2373030.2236205X-RAY DIFFRACTION100
2.789-2.9030.232980.2115967X-RAY DIFFRACTION100
2.903-3.0320.2353000.2095755X-RAY DIFFRACTION100
3.032-3.1790.1972970.1935466X-RAY DIFFRACTION99.9827
3.179-3.3510.2192640.1885244X-RAY DIFFRACTION100
3.351-3.5540.1892810.1714926X-RAY DIFFRACTION100
3.554-3.80.1882380.1644670X-RAY DIFFRACTION100
3.8-4.1040.1722000.1574383X-RAY DIFFRACTION100
4.104-4.4950.1592090.1464009X-RAY DIFFRACTION100
4.495-5.0250.1691820.1473684X-RAY DIFFRACTION100
5.025-5.8010.1861810.1613235X-RAY DIFFRACTION100
5.801-7.1010.2041480.1782766X-RAY DIFFRACTION100
7.101-10.0270.1561210.1412187X-RAY DIFFRACTION100
10.027-48.90.233630.1941253X-RAY DIFFRACTION97.6986

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