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- PDB-8fvd: E coli. CTP synthase in complex with dF-dCTP (potassium malonate ... -

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Basic information

Entry
Database: PDB / ID: 8fvd
TitleE coli. CTP synthase in complex with dF-dCTP (potassium malonate + 100 mM MgCl2)
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 (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
Chem-GTF / MALONIC ACID / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)122,1578
Polymers120,8942
Non-polymers1,2636
Water3,243180
1
A: CTP synthase
B: CTP synthase
hetero molecules

A: CTP synthase
B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,31416
Polymers241,7884
Non-polymers2,52612
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1,-y,z1
Buried area13440 Å2
ΔGint-110 kcal/mol
Surface area75970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)161.069, 110.013, 129.511
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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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-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 4.84 Å3/Da / Density % sol: 74.6 %
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: 0.9686 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.38→101 Å / Num. obs: 92195 / % possible obs: 100 % / Redundancy: 13.4 % / Biso Wilson estimate: 67.8 Å2 / CC1/2: 0.997 / CC star: 1 / Rmerge(I) obs: 0.19 / Rpim(I) all: 0.054 / Rrim(I) all: 0.198 / Net I/σ(I): 4.7
Reflection shellResolution: 2.38→2.47 Å / Redundancy: 13.2 % / Rmerge(I) obs: 2.631 / Mean I/σ(I) obs: 0.1 / Num. unique obs: 9010 / CC1/2: 0.692 / CC star: 0.927 / Rpim(I) all: 0.747 / Rrim(I) all: 2.736 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TKV

5tkv


Resolution: 2.38→100.93 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 31.5935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2324 3762 5.04 %
Rwork0.2087 70807 -
obs0.2099 74569 80.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 79.55 Å2
Refinement stepCycle: LAST / Resolution: 2.38→100.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8316 0 76 180 8572
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00198623
X-RAY DIFFRACTIONf_angle_d0.439311715
X-RAY DIFFRACTIONf_chiral_restr0.04271325
X-RAY DIFFRACTIONf_plane_restr0.00341526
X-RAY DIFFRACTIONf_dihedral_angle_d12.32453257
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.38-2.410.5961100.3941215X-RAY DIFFRACTION6.64
2.41-2.450.4844140.3993401X-RAY DIFFRACTION12.41
2.45-2.480.3037280.407559X-RAY DIFFRACTION17.47
2.48-2.510.4096430.3904726X-RAY DIFFRACTION22.85
2.51-2.550.3778560.3871248X-RAY DIFFRACTION38.5
2.55-2.590.3947850.39411552X-RAY DIFFRACTION48.71
2.59-2.630.41031120.39792141X-RAY DIFFRACTION66.09
2.63-2.680.36891500.37662559X-RAY DIFFRACTION80.39
2.68-2.730.38651520.37632823X-RAY DIFFRACTION87.94
2.73-2.780.34491510.36293134X-RAY DIFFRACTION96.42
2.78-2.840.35051640.3483160X-RAY DIFFRACTION98.4
2.84-2.90.33281570.33373245X-RAY DIFFRACTION99.88
2.9-2.970.35191640.33683227X-RAY DIFFRACTION99.91
2.97-3.040.35381850.32243243X-RAY DIFFRACTION99.97
3.04-3.120.34031720.29323198X-RAY DIFFRACTION99.91
3.12-3.220.27671790.25833217X-RAY DIFFRACTION99.91
3.22-3.320.26371580.23573257X-RAY DIFFRACTION99.97
3.32-3.440.26881860.22293233X-RAY DIFFRACTION99.97
3.44-3.580.22991800.21063217X-RAY DIFFRACTION99.94
3.58-3.740.20431890.19913249X-RAY DIFFRACTION99.97
3.74-3.940.23381810.18173244X-RAY DIFFRACTION99.94
3.94-4.180.19091680.16443279X-RAY DIFFRACTION99.91
4.18-4.50.18971650.14623268X-RAY DIFFRACTION99.83
4.5-4.960.17261600.14553291X-RAY DIFFRACTION99.77
4.96-5.670.17831900.1583295X-RAY DIFFRACTION99.91
5.68-7.150.2081670.19363352X-RAY DIFFRACTION99.94
7.15-100.930.19941960.17823474X-RAY DIFFRACTION99.48
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)
11.31471409160.591923395783-0.1470749149620.876313007434-0.6137453594551.430892610750.0224514903069-0.3266397820240.0712162069680.218481064983-0.165080626824-0.0379146399287-0.2037797960590.12898680097-4.56407893095E-50.523185089451-0.0837839402785-0.02038186354360.478166835778-0.04634239596940.447361171341-71.106784111813.2892309807-39.4660595025
20.983704484199-0.120971424755-0.06377142134781.314098775040.5781389015392.48894606207-0.003603735097670.1936673710810.217504406046-0.225289754043-0.045637301082-0.106992707918-0.3737938337450.2140039420382.77150313622E-50.471252189127-0.0602949372358-0.006265454503190.3969625812040.05970151554330.476020821421-66.880234364516.3724138835-58.8380938135
31.45049661045-0.296837479844-0.4924030160321.26590359203-1.183543091592.96588969129-0.174810582736-0.603341513075-0.2374260674210.365341577944-0.189034438766-0.307987941281-0.2352621402780.754184638649-0.005304916928550.622528361963-0.222462857595-0.144609740410.9668963693260.249167454710.6897750891-43.68432686769.70717279049-24.0638431171
41.109701371580.1423263101260.123923154740.247775636104-0.2782640291280.3899201070990.1183401710860.165657379725-0.0350825169563-0.240509714727-0.171170692739-0.1136943355590.2288893260870.2040258002831.49249641508E-50.60316339440.1041502919960.0285097182670.5401964770880.002760040704360.483129119934-64.7307727641-15.1846904437-78.1080231299
50.759457905994-0.00927975845365-0.9185993829240.793159755677-0.0486181642731.10499116824-0.161379800150.6403242747540.188050673815-0.154105449278-0.0141116443848-0.1494529324460.101537447260.1208445164820.0001134200527320.6503348003750.1317153807090.0005898991688120.642613164054-0.0388333456150.518130947817-66.4217282101-8.63877657343-89.4126360806
61.20318919826-0.772127496603-0.1811318720180.847535459287-0.3347433810690.725341618797-0.08370764972940.206842551546-0.284830890135-0.1223368796860.03051192848250.3421472130630.261882426066-0.0753085174247-0.0001201190428010.5267939430160.01585325185250.01293545192970.507854661341-0.0360874998250.522029748745-78.8827063497-12.3884704738-80.4966265425
71.29585400921-0.0327455765303-0.3250134325731.297393253621.058730214052.12213606586-0.0303309466788-0.310472344919-0.1165851648190.2242566512280.0146428250595-0.1804884156030.4177272861980.374516476529-7.59385572576E-50.6055748506220.09560708138920.01504228740330.4386986381040.07717617002620.526731031909-62.3845540341-14.9933740902-63.3144474287
81.39165731304-0.06868431655820.2197227618471.77570860612-0.3911394882111.91502076743-0.08855183795890.3232627970150.500754245907-0.2419458956730.0555455543451-0.283043422604-0.1746090066550.464479081753-0.0001478803241610.5884580709810.06649683021010.1235461604950.7629628995960.1467760248980.83363952756-43.0901696492-0.315526423927-97.4227980356
90.3497638667130.4567279796150.1188471253740.5816173282460.1893004504220.2159050064750.02586752504850.5195246387250.149946369371-0.1543177296050.0939892897205-0.1723329590.1438102817840.515635819042.96387475492E-60.8555032171350.2296719641120.1467278447381.054259943640.191334100890.633294932033-46.4786133563-9.01929381654-107.014973308
100.049365316866-0.06844926846940.04519076484810.654877522073-0.3586409877140.21530664918-0.1063444216990.8433291878380.252096732149-0.606224171693-0.0679862490837-0.1517735074650.7569514460771.208189781370.0001714878183890.8087752617240.147162826640.1721729486941.33341515390.1379718360770.778373371684-40.5699989762-8.07957032786-108.98340809
110.2487614839840.3517640152340.2792766183210.4807603241790.3633228616680.396808532369-0.2393434445120.7239945407770.096607730695-0.2091473329620.0923334670212-0.07077286235440.384229465470.3890713995120.000111955855810.6391810654460.1991094659640.08827967579570.9220886478020.09635324526290.719365644225-39.1631686195-10.484394041-92.6415774855
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 147 )AA1 - 1471 - 147
22chain 'A' and (resid 148 through 273 )AA148 - 273148 - 273
33chain 'A' and (resid 274 through 543 )AA274 - 543274 - 533
44chain 'B' and (resid 1 through 48 )BE1 - 481 - 48
55chain 'B' and (resid 49 through 105 )BE49 - 10549 - 105
66chain 'B' and (resid 106 through 164 )BE106 - 164106 - 164
77chain 'B' and (resid 165 through 273 )BE165 - 273165 - 273
88chain 'B' and (resid 274 through 452 )BE274 - 452274 - 443
99chain 'B' and (resid 453 through 482 )BE453 - 482444 - 473
1010chain 'B' and (resid 483 through 508 )BE483 - 508474 - 499
1111chain 'B' and (resid 509 through 543 )BE509 - 543500 - 534

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