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- PDB-4zdi: Crystal structure of the M. tuberculosis CTP synthase PyrG (apo form) -

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Basic information

Entry
Database: PDB / ID: 4zdi
TitleCrystal structure of the M. tuberculosis CTP synthase PyrG (apo form)
ComponentsCTP synthaseCTP synthetase
KeywordsLIGASE / CTP synthase / PyrG / amidotransferase
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / identical protein binding ...CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / ATP binding / metal ion binding / identical protein binding / plasma membrane / cytosol
Similarity search - Function
CTP synthase N-terminus / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases ...CTP synthase N-terminus / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesMycobacterium tuberculosis (unknown)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsBellinzoni, M. / Barilone, N. / Alzari, P.M.
Funding support France, 1items
OrganizationGrant numberCountry
European CommissionHEALTH-F3-2011-260872 France
CitationJournal: Chem.Biol. / Year: 2015
Title: Thiophenecarboxamide Derivatives Activated by EthA Kill Mycobacterium tuberculosis by Inhibiting the CTP Synthetase PyrG.
Authors: Mori, G. / Chiarelli, L.R. / Esposito, M. / Makarov, V. / Bellinzoni, M. / Hartkoorn, R.C. / Degiacomi, G. / Boldrin, F. / Ekins, S. / de Jesus Lopes Ribeiro, A.L. / Marino, L.B. / ...Authors: Mori, G. / Chiarelli, L.R. / Esposito, M. / Makarov, V. / Bellinzoni, M. / Hartkoorn, R.C. / Degiacomi, G. / Boldrin, F. / Ekins, S. / de Jesus Lopes Ribeiro, A.L. / Marino, L.B. / Centarova, I. / Svetlikova, Z. / Blasko, J. / Kazakova, E. / Lepioshkin, A. / Barilone, N. / Zanoni, G. / Porta, A. / Fondi, M. / Fani, R. / Baulard, A.R. / Mikusova, K. / Alzari, P.M. / Manganelli, R. / de Carvalho, L.P. / Riccardi, G. / Cole, S.T. / Pasca, M.R.
History
DepositionApr 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2015Group: Database references

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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
C: CTP synthase
D: CTP synthase
E: CTP synthase
F: CTP synthase
G: CTP synthase
H: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)510,48816
Polymers510,1688
Non-polymers3218
Water0
1
B: CTP synthase
hetero molecules

A: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6224
Polymers127,5422
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,-x,z+1/41
Buried area2458 Å2
ΔGint-27.4 kcal/mol
Surface area39935 Å2
MethodPISA
2
A: CTP synthase
hetero molecules

B: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6224
Polymers127,5422
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-y,x,z-1/41
Buried area2460 Å2
ΔGint-27 kcal/mol
Surface area39940 Å2
MethodPISA
3
C: CTP synthase
D: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6224
Polymers127,5422
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2940 Å2
ΔGint-33 kcal/mol
Surface area39080 Å2
MethodPISA
4
E: CTP synthase
H: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6224
Polymers127,5422
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-30 kcal/mol
Surface area39720 Å2
MethodPISA
5
F: CTP synthase
G: CTP synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,6224
Polymers127,5422
Non-polymers802
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2950 Å2
ΔGint-33 kcal/mol
Surface area39480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.826, 196.826, 184.047
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
CTP synthase / CTP synthetase / CTP synthetase / UTP--ammonia ligase


Mass: 63770.953 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (unknown)
Gene: pyrG, Rv1699, MTCI125.21 / Plasmid: pET-28a / Production host: Escherichia coli BL21(DE3) (unknown)
References: UniProt: P9WHK7, CTP synthase (glutamine hydrolysing)
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.5 Å3/Da / Density % sol: 64.8 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG8000, 200 mM Ca acetate, 100 mM Hepes pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 3.52→49.21 Å / Num. obs: 85758 / % possible obs: 98.4 % / Redundancy: 3.8 % / Biso Wilson estimate: 69.88 Å2 / Rmerge(I) obs: 0.137 / Net I/σ(I): 8.6
Reflection shellResolution: 3.52→3.58 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.998 / Mean I/σ(I) obs: 1.3 / % possible all: 92.1

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Processing

Software
NameVersionClassification
BUSTER2.10.1refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZDJ
Resolution: 3.52→49.21 Å / Cor.coef. Fo:Fc: 0.8712 / Cor.coef. Fo:Fc free: 0.8705 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.447
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 4288 5.01 %RANDOM
Rwork0.2128 ---
obs0.2132 85620 98.62 %-
Displacement parametersBiso mean: 111 Å2
Baniso -1Baniso -2Baniso -3
1-28.0945 Å20 Å20 Å2
2--28.0945 Å20 Å2
3----56.189 Å2
Refine analyzeLuzzati coordinate error obs: 0.81 Å
Refinement stepCycle: 1 / Resolution: 3.52→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30929 0 8 0 30937
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00831615HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.8943267HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d13921SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes638HARMONIC2
X-RAY DIFFRACTIONt_gen_planes4834HARMONIC5
X-RAY DIFFRACTIONt_it31615HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion1.65
X-RAY DIFFRACTIONt_other_torsion2.72
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion4321SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact35111SEMIHARMONIC4
LS refinement shellResolution: 3.52→3.61 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2577 323 5.14 %
Rwork0.2516 5962 -
all0.252 6285 -
obs--98.62 %
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.0878-0.74530.4741.29440.21082.16690.0226-0.02930.11190.10140.0882-0.09410.01270.0964-0.1108-0.0703-0.00190.10020.00070.034-0.152348.38336.9348-8.9464
20.2528-0.60451.568500.48171.84760.0041-0.0272-0.00790.06280.0216-0.01230.013-0.014-0.02570.03030.0461-0.07320.0798-0.0844-0.015364.125230.75748.6993
34.5499-1.3186-1.05123.0551.67591.7292-0.04080.138-0.0676-0.07510.0152-0.0357-0.0365-0.08030.0256-0.1090.06370.02130.02040.0601-0.188973.38512.5682-15.2181
42.3756-0.3942-0.49732.4137-0.43070.87170.02670.03170.1832-0.2621-0.0884-0.17620.13530.04520.06170.04620.09350.0914-0.055-0.0086-0.205546.5417-32.45482.9061
500.0693-2.83590.3656-2.25511.757700.03680.0182-0.01570.0042-0.00650.02390.0124-0.00410.04140.11630.14050.07250.0898-0.014950.242-17.2721-15.1092
62.7449-0.74950.10815.03410.18411.59770.02830.02670.0013-0.0928-0.2153-0.05740.1612-0.02990.1870.0120.0888-0.0128-0.03790.0376-0.296722.6155-7.0522-2.806
72.9950.38890.43541.9508-0.08981.1233-0.1340.07280.1545-0.19520.3083-0.0515-0.0030.0592-0.17430.0732-0.14330.03090.03390.0727-0.296449.29515.503235.4329
80.1317-0.06371.63370-1.28681.74290.00020.02420.001-0.02130.00740.0104-0.01070.0261-0.00770.1393-0.1211-0.07750.03880.1438-0.092833.40811.669217.8433
95.72781.8171-0.6642.9135-0.9551.1584-0.1437-0.0527-0.1857-0.03210.0435-0.0034-0.17640.0390.10020.029-0.07870.0054-0.04260.0078-0.263924.4023-9.173640.3607
101.1899-0.43010.48713.4896-0.07731.4018-0.0672-0.10580.1127-0.01320.1459-0.2815-0.0226-0.0442-0.0786-0.16090.152-0.08920.1278-0.1264-0.18866.594624.439166.2805
110.370.51611.22610.60192.29310.71190.0029-0.020.01210.04350.0072-0.0188-0.0293-0.0135-0.01010.02390.1051-0.11340.0269-0.13970.061983.443830.208883.0138
123.8502-1.272-0.13363.11750.14911.5549-0.06770.0248-0.0301-0.046-0.0279-0.068-0.052-0.1650.0956-0.16610.152-0.11550.1113-0.0384-0.206692.35691.210673.5752
131.22510.0984-0.56093.2057-0.442.0674-0.0746-0.14880.05870.09260.18290.23430.1042-0.013-0.1083-0.16550.1511-0.11190.0804-0.0692-0.120643.499452.542665.5275
140.1332-0.1722-1.07940.0357-1.00321.07210.0019-0.017-0.0050.04080.00320.010.00390.0166-0.00510.07320.07850.0480.02560.0772-0.003928.018548.831483.8902
153.0819-0.78160.25961.9347-0.41771.3825-0.0286-0.026-0.0168-0.0582-0.00130.087-0.0303-0.00240.0299-0.20720.1407-0.0391-0.034-0.13740.098418.056176.407271.5567
163.7244-0.0010.65011.55870.67041.90180.06220.1545-0.158-0.1309-0.0702-0.1403-0.0349-0.04320.008-0.06760.15190.1461-0.1337-0.0052-0.08574.3767-55.4831.7916
170.42380.44851.32030.2951.04361.72740.00180.0343-0.0029-0.02610.0053-0.0017-0.0219-0.0112-0.0070.03270.1058-0.04580.0551-0.09650.023368.9356-72.1675-15.2071
182.5991-2.5053-0.20434.04240.18360.5890.04270.04740.03840.0615-0.1615-0.1131-0.0663-0.07410.1189-0.07070.15120.1469-0.08070.0484-0.088797.9416-81.1464-5.5571
191.68610.2009-0.52141.62620.21972.36450.0282-0.11410.07340.183-0.0847-0.10460.01180.01070.05650.0305-0.07220.1294-0.1937-0.0598-0.027782.0221-38.286233.1303
200.0608-0.3549-1.10990.2690.96681.71110.001-0.037-0.00530.01340.01280.00490.0269-0.0185-0.01380.0336-0.03210.03880.0109-0.0813-0.000285.631-22.045750.6417
212.20490.6409-0.93243.6691-1.33510.62550.008-0.0221-0.004-0.061-0.0658-0.0860.0691-0.05280.0578-0.0465-0.14270.0068-0.196-0.07580.1153106.79-13.140828.807
221.67451.9609-1.00081.74211.28082.8817-0.1459-0.02720.0565-0.30890.3711-0.0797-0.1097-0.1157-0.22520.1003-0.152-0.1483-0.0741-0.0234-0.267858.533962.051331.2089
230.01660.6321-0.70090-0.5121.40280.00240.02660.0091-0.02430.0095-0.0188-0.0228-0.0208-0.0120.0663-0.14090.01660.0236-0.0797-0.066373.607367.502913.1746
244.33321.83310.53542.07630.75630.9979-0.1137-0.14480.1151-0.1960.1481-0.05060.0419-0.1068-0.03440.0822-0.152-0.0292-0.1363-0.1382-0.194684.355585.71337.245
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|7 - A|278 }
2X-RAY DIFFRACTION2{ A|279 - A|298 }
3X-RAY DIFFRACTION3{ A|299 - A|551 }
4X-RAY DIFFRACTION4{ B|7 - B|278 }
5X-RAY DIFFRACTION5{ B|279 - B|298 }
6X-RAY DIFFRACTION6{ B|299 - B|551 }
7X-RAY DIFFRACTION7{ C|7 - C|278 }
8X-RAY DIFFRACTION8{ C|279 - C|298 }
9X-RAY DIFFRACTION9{ C|299 - C|551 }
10X-RAY DIFFRACTION10{ D|7 - D|278 }
11X-RAY DIFFRACTION11{ D|279 - D|298 }
12X-RAY DIFFRACTION12{ D|299 - D|551 }
13X-RAY DIFFRACTION13{ E|7 - E|278 }
14X-RAY DIFFRACTION14{ E|279 - E|298 }
15X-RAY DIFFRACTION15{ E|299 - E|551 }
16X-RAY DIFFRACTION16{ F|6 - F|278 }
17X-RAY DIFFRACTION17{ F|279 - F|298 }
18X-RAY DIFFRACTION18{ F|299 - F|551 }
19X-RAY DIFFRACTION19{ G|7 - G|278 }
20X-RAY DIFFRACTION20{ G|279 - G|298 }
21X-RAY DIFFRACTION21{ G|299 - G|551 }
22X-RAY DIFFRACTION22{ H|7 - H|278 }
23X-RAY DIFFRACTION23{ H|279 - H|298 }
24X-RAY DIFFRACTION24{ H|299 - H|551 }

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