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- PDB-8fvb: E coli. CTP synthase in complex with CTP -

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Basic information

Entry
Database: PDB / ID: 8fvb
TitleE coli. CTP synthase in complex with CTP
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
CYTIDINE-5'-TRIPHOSPHATE / MALONIC ACID / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)122,2778
Polymers120,8942
Non-polymers1,3836
Water15,259847
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)244,55316
Polymers241,7884
Non-polymers2,76512
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area15210 Å2
ΔGint-94 kcal/mol
Surface area75820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.707, 103.907, 131.835
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-1088-

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-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O14P3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 847 / 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: 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: 2.03→44 Å / Num. obs: 142127 / % possible obs: 97.3 % / Redundancy: 14 % / Biso Wilson estimate: 33.4 Å2 / CC1/2: 0.97 / CC star: 0.992 / Rmerge(I) obs: 0.166 / Rpim(I) all: 0.045 / Rrim(I) all: 0.172 / Net I/σ(I): 4.83
Reflection shellResolution: 2.03→2.1 Å / Redundancy: 12.1 % / Rmerge(I) obs: 0.851 / Mean I/σ(I) obs: 1.15 / Num. unique obs: 10569 / CC1/2: 0.892 / CC star: 0.971 / Rpim(I) all: 0.248 / Rrim(I) all: 0.887 / % possible all: 73.4

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKV

5tkv


Resolution: 2.03→44 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.164 / SU ML: 0.086 / Cross valid method: FREE R-VALUE / ESU R: 0.125 / ESU R Free: 0.118
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2144 7162 5.039 %
Rwork0.1923 134965 -
all0.193 --
obs-142127 97.354 %
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: 35.822 Å2
Baniso -1Baniso -2Baniso -3
1-0.003 Å20 Å2-0 Å2
2---0.003 Å20 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 2.03→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8326 0 86 847 9259
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.0138773
X-RAY DIFFRACTIONr_bond_other_d0.0010.0178222
X-RAY DIFFRACTIONr_angle_refined_deg1.1581.64511944
X-RAY DIFFRACTIONr_angle_other_deg1.0921.57319096
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.57851124
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.32722.215474
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.859151523
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.361566
X-RAY DIFFRACTIONr_chiral_restr0.0440.21163
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.029900
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021800
X-RAY DIFFRACTIONr_nbd_refined0.1650.21617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.160.28077
X-RAY DIFFRACTIONr_nbtor_refined0.1410.24145
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0710.23600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1180.2841
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1730.236
X-RAY DIFFRACTIONr_nbd_other0.1680.2104
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0980.239
X-RAY DIFFRACTIONr_mcbond_it1.0373.7674345
X-RAY DIFFRACTIONr_mcbond_other1.0373.7664344
X-RAY DIFFRACTIONr_mcangle_it1.8575.6395446
X-RAY DIFFRACTIONr_mcangle_other1.8565.645447
X-RAY DIFFRACTIONr_scbond_it0.9163.8974426
X-RAY DIFFRACTIONr_scbond_other0.9163.9014415
X-RAY DIFFRACTIONr_scangle_it1.6155.7856472
X-RAY DIFFRACTIONr_scangle_other1.6145.7856473
X-RAY DIFFRACTIONr_lrange_it4.38345.0139892
X-RAY DIFFRACTIONr_lrange_other4.09244.4699627
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.031-2.0840.313400.2876494X-RAY DIFFRACTION64.0728
2.084-2.1410.2745350.2469891X-RAY DIFFRACTION100
2.141-2.2030.2894640.2339675X-RAY DIFFRACTION100
2.203-2.2710.2534760.2319396X-RAY DIFFRACTION99.9899
2.271-2.3450.2375090.2289018X-RAY DIFFRACTION99.9895
2.345-2.4270.2394840.2188804X-RAY DIFFRACTION100
2.427-2.5190.244460.2158444X-RAY DIFFRACTION99.9888
2.519-2.6220.2544350.2228203X-RAY DIFFRACTION100
2.622-2.7380.2424050.227873X-RAY DIFFRACTION99.9879
2.738-2.8720.2343870.2117501X-RAY DIFFRACTION99.9873
2.872-3.0270.2454040.2197121X-RAY DIFFRACTION100
3.027-3.2110.2183520.2026800X-RAY DIFFRACTION100
3.211-3.4320.1973660.1876364X-RAY DIFFRACTION100
3.432-3.7070.183060.1765973X-RAY DIFFRACTION100
3.707-4.060.1832740.1585525X-RAY DIFFRACTION100
4.06-4.5390.182440.1485019X-RAY DIFFRACTION99.981
4.539-5.240.1662590.1524421X-RAY DIFFRACTION99.9786
5.24-6.4160.182210.1753747X-RAY DIFFRACTION100
6.416-9.0620.2051530.1592982X-RAY DIFFRACTION100
9.062-440.2391020.2041714X-RAY DIFFRACTION98.6957

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