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- PDB-4wio: Crystal structure of the C89A GMP synthetase inactive mutant from... -

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Basic information

Entry
Database: PDB / ID: 4wio
TitleCrystal structure of the C89A GMP synthetase inactive mutant from Plasmodium falciparum in complex with glutamine
ComponentsGMP synthetase
KeywordsLIGASE / GMP synthetase / purine salvage pathway
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / Azathioprine ADME / GMP synthase (glutamine-hydrolyzing) activity / GMP synthase activity / GMP synthase (glutamine-hydrolysing) / purine nucleotide biosynthetic process / GMP biosynthetic 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 / GMP Synthetase; Chain A, domain 3 - #10 / 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 / GMP Synthetase; Chain A, domain 3 - #10 / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / GMP Synthetase; Chain A, domain 3 / Class I glutamine amidotransferase-like / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsBallut, L. / Violot, S. / Haser, R. / Aghajari, N.
CitationJournal: Nat Commun / Year: 2015
Title: Active site coupling in Plasmodium falciparum GMP synthetase is triggered by domain rotation.
Authors: Ballut, L. / Violot, S. / Shivakumaraswamy, S. / Thota, L.P. / Sathya, M. / Kunala, J. / Dijkstra, B.W. / Terreux, R. / Haser, R. / Balaram, H. / Aghajari, N.
History
DepositionSep 26, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Dec 2, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4592
Polymers65,3121
Non-polymers1461
Water724
1
A: GMP synthetase
hetero molecules

A: GMP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,9174
Polymers130,6252
Non-polymers2922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area2360 Å2
ΔGint-18 kcal/mol
Surface area43920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.920, 76.920, 204.780
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein GMP synthetase


Mass: 65312.367 Da / Num. of mol.: 1 / Fragment: UNP residues 2-555 / Mutation: C89A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF10_0123 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IJR9, GMP synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-GLN / GLUTAMINE


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1 M Tris-HCl pH 8.5, 22.5% (w/v) PEG 1000 and 10 mM Gln

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07812 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07812 Å / Relative weight: 1
ReflectionResolution: 3.15→61.5 Å / Num. obs: 11311 / % possible obs: 99.9 % / Redundancy: 7.5 % / Net I/σ(I): 10.1
Reflection shellResolution: 3.47→3.97 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3.92 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8_1069)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UOW

3uow


Resolution: 3.15→48.03 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 2.03 / Phase error: 35.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3062 563 4.99 %
Rwork0.2629 --
obs0.2652 11287 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.15→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4024 0 10 4 4038
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034119
X-RAY DIFFRACTIONf_angle_d0.6385607
X-RAY DIFFRACTIONf_dihedral_angle_d10.2841425
X-RAY DIFFRACTIONf_chiral_restr0.045646
X-RAY DIFFRACTIONf_plane_restr0.002727
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.470.3841370.32762614X-RAY DIFFRACTION100
3.47-3.970.32151370.28272619X-RAY DIFFRACTION100
3.97-4.990.29421390.25472657X-RAY DIFFRACTION100

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