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- PDB-7zu9: CRYSTAL STRUCTURE OF THE C89A_C113A GMP SYNTHETASE INACTIVE DOUBL... -

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Basic information

Entry
Database: PDB / ID: 7zu9
TitleCRYSTAL STRUCTURE OF THE C89A_C113A GMP SYNTHETASE INACTIVE DOUBLE MUTANT FROM PLASMODIUM FALCIPARUM
ComponentsGlutamine amidotransferase
KeywordsLIGASE / GMP SYNTHETASE / PURINE SALVAGE PATHWAY
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / Azathioprine ADME / GMP synthase activity / GMP synthase (glutamine-hydrolyzing) activity / GMP synthase (glutamine-hydrolysing) / GMP biosynthetic process / purine nucleotide biosynthetic process / glutamine metabolic process / magnesium ion binding / ATP binding / cytosol
Similarity search - Function
GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase ...GMP synthase / GMP synthase, C-terminal / GMP synthetase ATP pyrophosphatase domain / GMP synthase C terminal domain / GMP synthetase ATP pyrophosphatase (GMPS ATP-PPase) domain profile. / GMP synthase, glutamine amidotransferase / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / Rossmann-like alpha/beta/alpha sandwich fold
Similarity search - Domain/homology
GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsBallut, L. / Violot, S. / Aghajari, N.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-17-CE11-0032 France
CitationJournal: Biomolecules / Year: 2022
Title: Tertiary and Quaternary Structure Organization in GMP Synthetases: Implications for Catalysis.
Authors: Ballut, L. / Violot, S. / Galisson, F. / Goncalves, I.R. / Martin, J. / Shivakumaraswamy, S. / Carrique, L. / Balaram, H. / Aghajari, N.
History
DepositionMay 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2023Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2Feb 7, 2024Group: 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
A: Glutamine amidotransferase


Theoretical massNumber of molelcules
Total (without water)65,4231
Polymers65,4231
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, A
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area26040 Å2
Unit cell
Length a, b, c (Å)111.650, 64.540, 56.330
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Glutamine amidotransferase /


Mass: 65423.477 Da / Num. of mol.: 1 / Mutation: C89A and C113A
Source method: isolated from a genetically manipulated source
Details: The studied GMP synthetase has been mutated on Cys89 to Ala and on Cys113 to Ala
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Strain: isolate 3D7 / Gene: PF3D7_1012600 / Plasmid: PET21B / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IJR9, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / 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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 16 % polyethylene glycol (PEG) 3350, 0.06 M sodium citrate (pH 2.3) and 0.04 M Bis-Tris propane (pH 9.7)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.8729 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8729 Å / Relative weight: 1
ReflectionResolution: 2.8→28.16 Å / Num. obs: 9228 / % possible obs: 92.3 % / Redundancy: 2.6 % / CC1/2: 0.99 / Net I/σ(I): 9.3
Reflection shellResolution: 2.8→3.2 Å / Num. unique obs: 2928 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WIO, 4WIM, 4WIN

4wio

4wim

4win


Resolution: 2.8→28.16 Å / Cross valid method: FREE R-VALUE / σ(F): 2.35 / Phase error: 30.39 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3139 475 5.15 %
Rwork0.2701 --
obs0.2739 9222 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.8→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4074 0 0 10 4084
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005
X-RAY DIFFRACTIONf_angle_d1.005
X-RAY DIFFRACTIONf_dihedral_angle_d8.931546
X-RAY DIFFRACTIONf_chiral_restr0.058624
X-RAY DIFFRACTIONf_plane_restr0.008717
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8-3.20.42581550.32762928X-RAY DIFFRACTION89
3.2-4.040.2981530.26032924X-RAY DIFFRACTION88
4.04-28.160.28661540.26172908X-RAY DIFFRACTION86
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)
11.5905-0.9802-0.01552.21650.28920.1740.02640.2352-0.27250.585-0.01610.244-0.0964-0.1447-0.060.3512-0.00990.03120.2508-0.01460.14541.7075-6.9424-6.7732
20.21010.07080.27640.0440.10840.37060.0599-0.1438-0.004-0.1281-0.0786-0.01290.1063-0.1897-0.08420.19980.0170.07180.18490.0660.166242.2963-4.227311.6858
30.4932-0.4424-0.32220.7950.56960.40620.0643-0.001-0.04920.0841-0.0990.18550.12070.04590.1470.43450.08370.14750.4282-0.0190.20579.6967-5.37528.5718
40.6765-0.52210.04790.41450.07531.1435-0.1738-0.0206-0.13880.12750.3111-0.114-0.3376-0.1079-0.07370.3185-0.01740.08740.21070.0240.32428.3077-6.569323.6717
50.28290.18860.2330.4219-0.11490.9490.0164-0.0135-0.02690.0528-0.12280.05230.1614-0.18510.09340.37790.03730.08360.1603-0.10620.345913.8361-0.084420.0429
60.03870.0761-0.24891.0369-1.16172.31870.0756-0.24810.0138-0.191-0.32790.15260.755-0.26270.13940.3278-0.0550.06720.3636-0.00170.305526.94348.20229.4815
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 6 through 41 )
2X-RAY DIFFRACTION2chain 'A' and (resid 42 through 218 )
3X-RAY DIFFRACTION3chain 'A' and (resid 219 through 299 )
4X-RAY DIFFRACTION4chain 'A' and (resid 300 through 386 )
5X-RAY DIFFRACTION5chain 'A' and (resid 387 through 456 )
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 554 )

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