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- PDB-8fv9: E coli. CTP synthase in complex with F-dCTP -

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Basic information

Entry
Database: PDB / ID: 8fv9
TitleE coli. CTP synthase in complex with F-dCTP
ComponentsCTP synthaseCTP synthetase
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 / glutaminase activity / glutamine metabolic process / ATP binding / metal ion binding
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-80J / MALONIC ACID / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.991 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 2.0Jun 14, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Experimental preparation
Category: atom_site / citation ...atom_site / citation / citation_author / exptl_crystal / pdbx_nonpoly_scheme
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID / _exptl_crystal.density_meas / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,2808
Polymers120,8942
Non-polymers1,3876
Water14,808822
1
AAA: CTP synthase
BBB: CTP synthase
hetero molecules

AAA: CTP synthase
BBB: CTP synthase
hetero molecules


  • defined by author&software
  • 245 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)244,56116
Polymers241,7884
Non-polymers2,77312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area13480 Å2
ΔGint-90 kcal/mol
Surface area75990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.419, 103.506, 131.562
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-1091-

HOH

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Components

#1: Protein CTP synthase / CTP synthetase / 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 / Malonic acid


Mass: 104.061 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H4O4
#3: Chemical ChemComp-80J / 2'-deoxy-2'-fluorocytidine 5'-(tetrahydrogen triphosphate)


Mass: 485.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H15FN3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 822 / 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 meas: 73.43 Mg/m3
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: 0.978 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: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.99→43.8 Å / Num. obs: 152954 / % possible obs: 99.6 % / Redundancy: 14.4 % / Biso Wilson estimate: 33.6 Å2 / CC1/2: 0.96 / CC star: 0.648 / Rmerge(I) obs: 0.124 / Rpim(I) all: 0.033 / Rrim(I) all: 0.129 / Net I/σ(I): 16.8
Reflection shellResolution: 1.99→2.06 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.878 / Mean I/σ(I) obs: 1.98 / Num. unique obs: 14592 / CC1/2: 0.648 / CC star: 0.887 / Rpim(I) all: 0.346 / Rrim(I) all: 0.95 / % possible all: 96.1

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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: 1.991→43.8 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 2.874 / SU ML: 0.079 / Cross valid method: FREE R-VALUE / ESU R: 0.114 / ESU R Free: 0.106
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2049 7768 5.079 %
Rwork0.1904 145186 -
all0.191 --
obs-152954 99.573 %
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: 36.084 Å2
Baniso -1Baniso -2Baniso -3
1-0.006 Å20 Å2-0 Å2
2---0.008 Å20 Å2
3---0.002 Å2
Refinement stepCycle: LAST / Resolution: 1.991→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8312 0 86 822 9220
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0138770
X-RAY DIFFRACTIONr_bond_other_d0.0010.0158408
X-RAY DIFFRACTIONr_angle_refined_deg1.1651.6511940
X-RAY DIFFRACTIONr_angle_other_deg1.0981.5819382
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5551126
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62522.135473
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.867151527
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.7531567
X-RAY DIFFRACTIONr_chiral_restr0.0460.21158
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210015
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021981
X-RAY DIFFRACTIONr_nbd_refined0.1660.21625
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1550.28268
X-RAY DIFFRACTIONr_nbtor_refined0.1420.24137
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0680.24015
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1110.2784
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0060.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.221
X-RAY DIFFRACTIONr_nbd_other0.1430.2106
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.10.237
X-RAY DIFFRACTIONr_mcbond_it1.0593.7314347
X-RAY DIFFRACTIONr_mcbond_other1.0593.734346
X-RAY DIFFRACTIONr_mcangle_it1.8645.5865452
X-RAY DIFFRACTIONr_mcangle_other1.8645.5865453
X-RAY DIFFRACTIONr_scbond_it1.0033.8874421
X-RAY DIFFRACTIONr_scbond_other1.0033.8914410
X-RAY DIFFRACTIONr_scangle_it1.7515.7646462
X-RAY DIFFRACTIONr_scangle_other1.755.7646463
X-RAY DIFFRACTIONr_lrange_it4.19144.5969821
X-RAY DIFFRACTIONr_lrange_other3.93844.0919601
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.991-2.0430.2635350.26110101X-RAY DIFFRACTION94.7022
2.043-2.0990.2475720.2410360X-RAY DIFFRACTION100
2.099-2.160.255490.23310153X-RAY DIFFRACTION99.9907
2.16-2.2260.235110.2199840X-RAY DIFFRACTION100
2.226-2.2990.2334920.2189604X-RAY DIFFRACTION100
2.299-2.380.2344930.2149199X-RAY DIFFRACTION100
2.38-2.470.2154620.2068970X-RAY DIFFRACTION99.9894
2.47-2.5710.2224660.2138597X-RAY DIFFRACTION100
2.571-2.6850.2464420.228214X-RAY DIFFRACTION100
2.685-2.8160.2394120.2177945X-RAY DIFFRACTION99.988
2.816-2.9680.2363820.2157535X-RAY DIFFRACTION100
2.968-3.1480.2353790.217149X-RAY DIFFRACTION99.9734
3.148-3.3650.2033630.1876701X-RAY DIFFRACTION100
3.365-3.6350.2013650.1786231X-RAY DIFFRACTION99.9697
3.635-3.9810.1723090.165810X-RAY DIFFRACTION100
3.981-4.4510.1732720.155228X-RAY DIFFRACTION99.9818
4.451-5.1380.1552780.1464654X-RAY DIFFRACTION99.9797
5.138-6.2910.1672290.1653966X-RAY DIFFRACTION100
6.291-8.8860.1641670.1653124X-RAY DIFFRACTION100
8.886-43.80.231900.2071805X-RAY DIFFRACTION98.5952

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