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- PDB-8sbr: E coli. CTP synthase in complex with CTP (sodium malonate + 20 mM... -

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Basic information

Entry
Database: PDB / ID: 8sbr
TitleE coli. CTP synthase in complex with CTP (sodium malonate + 20 mM MgCl2)
ComponentsCTP synthase
KeywordsCYTOSOLIC PROTEIN / LIGASE/PRODUCT / Inhibitor complex / Metabolic enzyme / LIGASE / LIGASE-PRODUCT complex
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 (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases ...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 (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
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: 2.59 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
DepositionApr 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 24, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 7, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,0686
Polymers120,8942
Non-polymers1,1744
Water2,486138
1
A: CTP synthase
B: CTP synthase
hetero molecules

A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,13712
Polymers241,7884
Non-polymers2,3498
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area14350 Å2
ΔGint-81 kcal/mol
Surface area78550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)163.324, 106.782, 132.825
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab

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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-CTP / CYTIDINE-5'-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


Mass: 18.015 Da / Num. of mol.: 138 / 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: CHESS / Beamline: 7B2 / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 2.59→163.74 Å / Num. obs: 72255 / % possible obs: 99.5 % / Redundancy: 11.2 % / Biso Wilson estimate: 55.18 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.245 / Rpim(I) all: 0.075 / Rrim(I) all: 0.256 / Net I/σ(I): 5.6
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 11.89 % / Rmerge(I) obs: 1.81 / Num. unique obs: 3535 / CC1/2: 0.88 / Rpim(I) all: 0.546 / Rrim(I) all: 1.891 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.59→132.82 Å / SU ML: 0.4013 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.7801
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2433 3649 5.07 %
Rwork0.2122 68340 -
obs0.2137 71989 99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.87 Å2
Refinement stepCycle: LAST / Resolution: 2.59→132.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8331 0 72 138 8541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00148601
X-RAY DIFFRACTIONf_angle_d0.449511675
X-RAY DIFFRACTIONf_chiral_restr0.04231327
X-RAY DIFFRACTIONf_plane_restr0.00381523
X-RAY DIFFRACTIONf_dihedral_angle_d11.18633237
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.630.43741160.39712475X-RAY DIFFRACTION94.49
2.63-2.660.34411310.33672634X-RAY DIFFRACTION99.64
2.66-2.70.33121330.31782606X-RAY DIFFRACTION99.71
2.7-2.740.32731500.30482627X-RAY DIFFRACTION99.78
2.74-2.780.32251440.31272575X-RAY DIFFRACTION99.49
2.78-2.830.37121260.30772635X-RAY DIFFRACTION99.71
2.83-2.880.32961380.31262615X-RAY DIFFRACTION99.75
2.88-2.930.38761500.30892597X-RAY DIFFRACTION99.75
2.93-2.990.371280.31172653X-RAY DIFFRACTION99.64
2.99-3.050.33891400.28862634X-RAY DIFFRACTION99.78
3.05-3.110.30731330.27512607X-RAY DIFFRACTION99.53
3.11-3.190.31351360.26612629X-RAY DIFFRACTION99.5
3.19-3.270.30411570.26172617X-RAY DIFFRACTION99.46
3.27-3.350.23431310.24762625X-RAY DIFFRACTION99.46
3.35-3.450.29051350.24552621X-RAY DIFFRACTION99.35
3.45-3.560.2781350.2512607X-RAY DIFFRACTION98.28
3.56-3.690.2711610.24552612X-RAY DIFFRACTION98.47
3.69-3.840.25171490.22582X-RAY DIFFRACTION98.59
3.84-4.010.20351700.18572560X-RAY DIFFRACTION97.67
4.01-4.230.2111440.18052602X-RAY DIFFRACTION97.65
4.23-4.490.20021440.16322614X-RAY DIFFRACTION97.91
4.49-4.840.17721370.15112634X-RAY DIFFRACTION98.37
4.84-5.320.16341150.14812693X-RAY DIFFRACTION99.01
5.33-6.10.19641580.17052684X-RAY DIFFRACTION99.61
6.1-7.680.23321420.17072733X-RAY DIFFRACTION99.83
7.68-132.820.17121460.15912869X-RAY DIFFRACTION99.54
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.18359756581-0.7723776083511.07953306471.059059455480.2806530716441.07916333363-0.0002737214729520.3307454237290.111170533106-0.110402137404-0.0778915236631-0.0428201041366-0.2076697178-0.1435598177530.08339810054060.382141468340.0720322772492-0.00776318558940.5488660925150.05565480075960.2073008995-11.670952470411.1357686364-20.2781800852
22.01079354540.110976509115-0.3601379004632.14576705111-0.6850501209412.028982130650.0381717341847-0.1223114496960.2031156596720.170320952996-0.05594864699630.0425185774106-0.348510467579-0.1799169058290.02345248242920.3741857664680.0631739426295-0.05101603095090.559192224968-0.06256639663450.207984414409-16.375363487914.1939135003-1.74244295825
31.59562190848-0.201094665977-0.1712295095981.851586143660.5985718310062.20130841407-0.004646725965330.343808704241-0.421746323762-0.1838353871780.02523711085470.139319767390.189630758932-0.415879029785-0.02366519976040.3991677703010.0823305028911-0.08081692136470.803973173304-0.0884020830720.397737693473-37.35568985232.50557411185-35.8285189691
42.195644699960.3452383753430.07573786058310.8319097737150.1113780477861.896410878030.101809334836-0.166365980593-0.29051434236-0.0224413429631-0.0678159238441-0.09592544265960.387485664016-0.0919125181836-0.01305439489510.375445112186-0.0498048571897-0.007267752776040.4749923518470.03351091351470.256215254703-11.7242646348-14.990780558816.7678701663
51.510948754640.00612960663396-0.00587515245042.220372334140.705051934962.04467179281-0.0954917954991-0.3355238610640.3110617046130.1117469515510.0207105672330.076963596293-0.275990299118-0.7604163981020.07709769619360.417489167442-0.0998965476591-0.01569438305781.01001533873-0.07355262091490.354560327035-36.3093242266-9.7943930725142.261144158
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 131 )AA1 - 1311 - 131
22chain 'A' and (resid 132 through 273 )AA132 - 273132 - 273
33chain 'A' and (resid 274 through 544 )AA274 - 544274 - 535
44chain 'B' and (resid 1 through 273 )BD1 - 2731 - 273
55chain 'B' and (resid 274 through 543 )BD274 - 543274 - 534

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