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- PDB-3nva: Dimeric form of CTP synthase from Sulfolobus solfataricus -

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Basic information

Entry
Database: PDB / ID: 3nva
TitleDimeric form of CTP synthase from Sulfolobus solfataricus
ComponentsCTP synthaseCTP synthetase
KeywordsLIGASE / Rossmann fold / CTP synthase activity / nucleotide binding
Function / homology
Function and homology information


CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein 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 (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 class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / 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 speciesSulfolobus solfataricus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.504 Å
AuthorsHarris, P. / Willemoes, M. / Lauritsen, I. / Johansson, E. / Jensen, K.F.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2011
Title: Structure of the dimeric form of CTP synthase from Sulfolobus solfataricus
Authors: Lauritsen, I. / Willemoes, M. / Jensen, K.F. / Johansson, E. / Harris, P.
History
DepositionJul 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 25, 2012Group: Database references
Revision 1.3Nov 12, 2014Group: Structure summary
Revision 1.4May 23, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.5Nov 1, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CTP synthase
B: CTP synthase


Theoretical massNumber of molelcules
Total (without water)119,6672
Polymers119,6672
Non-polymers00
Water2,648147
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-17 kcal/mol
Surface area42300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.450, 76.780, 98.870
Angle α, β, γ (deg.)100.990, 95.360, 108.420
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 59833.672 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (archaea) / Gene: pyrG, SSO0201 / Production host: Escherichia coli (E. coli)
References: UniProt: Q980S6, CTP synthase (glutamine hydrolysing)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O

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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: 2.53 Å3/Da / Density % sol: 51.42 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 6% PEG 8000, 0.1M magnesium acetate, 0.1M sodium acetate buffer pH 4.5 , VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: May 5, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04 Å / Relative weight: 1
ReflectionResolution: 2.5→27.392 Å / Num. obs: 39001 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.979 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 19.93
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.5-2.60.3750.2854.715232454839300.3386.4
2.6-2.80.2420.1866.827601715469410.21597
2.8-30.1380.11510.421051544652880.13397.1
3-40.0510.0521.35227613613132570.05897.4
4-50.0230.03137.918209481447130.03697.9
5-60.0220.03139.28054215121080.03798
6-100.0210.0341.28449230422500.03597.7
10-200.0210.02839.316326385140.03480.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.74 Å28.74 Å
Translation2.74 Å28.74 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
PHENIX1.6.2_432refinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCN

1vcn


Resolution: 2.504→27.392 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.7673 / SU ML: 0.48 / σ(F): 1.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1948 5 %RANDOM
Rwork0.2068 ---
all0.2106 39001 --
obs0.2105 38978 96.47 %-
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 65.016 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso max: 208.53 Å2 / Biso mean: 60.9652 Å2 / Biso min: 13.17 Å2
Baniso -1Baniso -2Baniso -3
1-6.0189 Å2-1.7991 Å26.4966 Å2
2--4.7526 Å2-3.1867 Å2
3----10.7715 Å2
Refinement stepCycle: LAST / Resolution: 2.504→27.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8382 0 0 147 8529
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0098532
X-RAY DIFFRACTIONf_angle_d1.18211550
X-RAY DIFFRACTIONf_chiral_restr0.0741344
X-RAY DIFFRACTIONf_plane_restr0.0051472
X-RAY DIFFRACTIONf_dihedral_angle_d22.5985332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5041-2.59360.43231830.32323485366890
2.5936-2.69730.35111950.28813706390197
2.6973-2.820.43471960.27133734393097
2.82-2.96850.34991950.24653704389997
2.9685-3.15420.3241980.23973744394297
3.1542-3.39730.29821980.22153764396298
3.3973-3.73850.29611950.21573717391297
3.7385-4.27770.26151980.18873754395298
4.2777-5.38270.23021980.16463768396698
5.3827-27.39360.22211920.17283654384696
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)
11.3010.0022-0.91632.00410.00954.3930.0589-0.1170.0702-0.083-0.06530.50310.80080.79010.09960.15510.1097-0.01880.12460.0850.27069.3581-13.3699-1.9831
2-0.09330.00850.33360.2325-0.05432.5118-0.12030.08580.0725-0.00810.0536-0.05660.20050.35150.04150.1250.0363-0.00610.2155-0.0050.21075.7882-9.3962-13.4916
30.254-0.2108-0.43780.59330.05442.2737-0.0797-0.2032-0.0650.1947-0.03540.0440.99480.37180.14080.45880.17230.02690.2070.06040.2567.2517-21.36065.086
40.1729-0.292-0.22620.47910.17690.254-0.0432-0.05340.05440.3498-0.2079-0.00880.1717-0.04240.13730.2045-0.06420.06260.1688-0.10730.2297-12.39323.707310.9318
50.38440.0340.33440.6771-0.77641.19710.017-0.34340.1820.3433-0.4409-0.2392-0.7306-0.2470.09870.31990.44770.0288-0.049-0.00010.2401-16.114319.21710.2851
60.8225-0.0943-0.35440.1129-0.3371.3080.1976-0.02660.13380.147-0.01390.0968-0.83920.0231-0.17110.46170.00320.04810.0347-0.00190.3062-1.194918.23294.2741
70.38970.111-0.76251.7084-0.2731.8795-0.20290.3091-0.0772-0.023-0.5068-0.18030.7979-0.95460.47470.3862-0.40280.16170.7313-0.15760.3158-15.085-24.8537-43.59
8-0.02310.05260.35860.1890.55372.1681-0.2209-0.0560.04880.0653-0.20610.09090.255-0.69940.33970.1377-0.0950.02050.3937-0.06610.1859-11.9681-13.6033-35.463
90.73470.0738-0.66340.7878-0.05742.5076-0.110.3337-0.1728-0.0002-0.20410.02981.7352-0.87210.27320.9864-0.45140.16240.4655-0.13130.2809-12.351-35.1751-44.9719
101.07370.515-0.46551.0395-0.40481.4643-0.2846-0.3014-0.2786-0.2508-0.26270.05280.48060.05460.31020.16780.09730.03920.20960.08210.13016.3007-15.8293-63.4452
110.20860.2364-0.51690.9124-0.62661.1208-0.0717-0.3347-0.124-0.0603-0.36730.02870.03610.35950.31730.1406-0.0493-0.01240.34540.03840.25929.49682.9714-62.2891
120.35070.2186-0.170.5899-0.09260.5336-0.0539-0.11210.0932-0.14450.02390.2490.0018-0.31940.00390.16010.0659-0.06940.30720.01750.2234-5.2738-0.2614-64.9364
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN A AND RESID 2:31)A2 - 31
2X-RAY DIFFRACTION2(CHAIN A AND RESID 32:183)A32 - 183
3X-RAY DIFFRACTION3(CHAIN A AND RESID 184:294)A184 - 294
4X-RAY DIFFRACTION4(CHAIN A AND RESID 295:361)A295 - 361
5X-RAY DIFFRACTION5(CHAIN A AND RESID 362:435)A362 - 435
6X-RAY DIFFRACTION6(CHAIN A AND RESID 436:534)A436 - 534
7X-RAY DIFFRACTION7(CHAIN B AND RESID 2:31)B2 - 31
8X-RAY DIFFRACTION8(CHAIN B AND RESID 32:169)B32 - 169
9X-RAY DIFFRACTION9(CHAIN B AND RESID 170:294)B170 - 294
10X-RAY DIFFRACTION10(CHAIN B AND RESID 295:362)B295 - 362
11X-RAY DIFFRACTION11(CHAIN B AND RESID 363:435)B363 - 435
12X-RAY DIFFRACTION12(CHAIN B AND RESID 436:534)B436 - 534

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