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- PDB-8fv7: E coli. CTP synthase in complex with dF-dCTP + ATP -

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Basic information

Entry
Database: PDB / ID: 8fv7
TitleE coli. CTP synthase in complex with dF-dCTP + ATP
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
ADENOSINE-5'-TRIPHOSPHATE / Chem-GTF / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 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 1.2Oct 25, 2023Group: 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)123,00710
Polymers120,8942
Non-polymers2,1138
Water11,872659
1
AAA: CTP synthase
BBB: CTP synthase
hetero molecules

AAA: CTP synthase
BBB: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)246,01320
Polymers241,7884
Non-polymers4,22516
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area17380 Å2
ΔGint-172 kcal/mol
Surface area73300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.982, 108.456, 128.900
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-996-

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-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 659 / 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: 1.6532 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6532 Å / Relative weight: 1
ReflectionResolution: 2.08→83.126 Å / Num. obs: 133846 / % possible obs: 100 % / Redundancy: 12.5 % / Biso Wilson estimate: 35.3 Å2 / CC1/2: 0.994 / CC star: 0.999 / Rmerge(I) obs: 0.135 / Rpim(I) all: 0.04 / Rrim(I) all: 0.141 / Net I/σ(I): 12.4
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 12 % / Rmerge(I) obs: 1.862 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 13223 / CC1/2: 0.684 / CC star: 0.901 / Rpim(I) all: 0.556 / Rrim(I) all: 1.944 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKV

5tkv


Resolution: 2.08→83.126 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.299 / SU ML: 0.108 / Cross valid method: FREE R-VALUE / ESU R: 0.139 / ESU R Free: 0.127
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2215 6615 4.946 %
Rwork0.203 127125 -
all0.204 --
obs-133740 99.81 %
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: 39.846 Å2
Baniso -1Baniso -2Baniso -3
1--1.406 Å2-0 Å20 Å2
2--2.187 Å2-0 Å2
3----0.781 Å2
Refinement stepCycle: LAST / Resolution: 2.08→83.126 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8334 0 126 659 9119
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0138859
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158482
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.64412073
X-RAY DIFFRACTIONr_angle_other_deg1.0971.57719530
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72751126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.23521.822472
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.6151537
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4541571
X-RAY DIFFRACTIONr_chiral_restr0.0450.21172
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210088
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022010
X-RAY DIFFRACTIONr_nbd_refined0.170.21610
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1590.28385
X-RAY DIFFRACTIONr_nbtor_refined0.1430.24219
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.24018
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2685
X-RAY DIFFRACTIONr_metal_ion_refined0.1110.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0970.216
X-RAY DIFFRACTIONr_nbd_other0.1560.2105
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.230
X-RAY DIFFRACTIONr_mcbond_it1.3424.1324393
X-RAY DIFFRACTIONr_mcbond_other1.3424.1314392
X-RAY DIFFRACTIONr_mcangle_it2.3446.195523
X-RAY DIFFRACTIONr_mcangle_other2.3446.195524
X-RAY DIFFRACTIONr_scbond_it1.3514.3154466
X-RAY DIFFRACTIONr_scbond_other1.3514.3144467
X-RAY DIFFRACTIONr_scangle_it2.3476.3896539
X-RAY DIFFRACTIONr_scangle_other2.3476.3886540
X-RAY DIFFRACTIONr_lrange_it4.71348.8519802
X-RAY DIFFRACTIONr_lrange_other4.49848.4339611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.08-2.1340.3034530.3039358X-RAY DIFFRACTION99.9593
2.134-2.1930.2784460.2779091X-RAY DIFFRACTION99.9686
2.193-2.2560.264510.2658867X-RAY DIFFRACTION99.9464
2.256-2.3250.2814630.2528538X-RAY DIFFRACTION99.9223
2.325-2.4020.2954410.2428371X-RAY DIFFRACTION99.9546
2.402-2.4860.2524240.2348045X-RAY DIFFRACTION99.9646
2.486-2.580.2484050.2277803X-RAY DIFFRACTION99.9756
2.58-2.6850.263720.2257537X-RAY DIFFRACTION99.9621
2.685-2.8040.2623750.2267208X-RAY DIFFRACTION99.9868
2.804-2.9410.2483760.2186878X-RAY DIFFRACTION99.9724
2.941-3.10.2173420.2226584X-RAY DIFFRACTION99.9856
3.1-3.2880.2373170.26210X-RAY DIFFRACTION99.847
3.288-3.5150.2213160.195838X-RAY DIFFRACTION99.7569
3.515-3.7970.22930.1765468X-RAY DIFFRACTION99.7576
3.797-4.1590.1932530.1655032X-RAY DIFFRACTION99.6606
4.159-4.6490.1712430.1514568X-RAY DIFFRACTION99.4008
4.649-5.3680.162130.1564048X-RAY DIFFRACTION99.4167
5.368-6.5730.1982150.1893414X-RAY DIFFRACTION99.343
6.573-9.2870.1641330.1682731X-RAY DIFFRACTION99.0318
9.287-83.1260.257840.2691536X-RAY DIFFRACTION96.6011

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