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- PDB-4win: Crystal structure of the GATase domain from Plasmodium falciparum... -

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Basic information

Entry
Database: PDB / ID: 4win
TitleCrystal structure of the GATase domain from Plasmodium falciparum GMP synthetase
ComponentsGMP synthetase
KeywordsTRANSFERASE / GMP synthetase / Plasmodium falciparum / purine salvage pathway / glutamine amidotransferase
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 / Glutamine amidotransferase / Glutamine amidotransferase class-I ...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 / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase (GATase) domain / Class I glutamine amidotransferase-like / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NITRATE ION / GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GMP synthetase
B: GMP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,8455
Polymers57,6592
Non-polymers1863
Water1,67593
1
A: GMP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9543
Polymers28,8301
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GMP synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8922
Polymers28,8301
Non-polymers621
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.820, 74.210, 91.590
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein GMP synthetase


Mass: 28829.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Strain: isolate 3D7 / Gene: PF10_0123 / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IJR9, GMP synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7.4 / Details: 0.2 M Lithium Nitrate and 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.93928 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93928 Å / Relative weight: 1
ReflectionResolution: 2.6→56 Å / Num. obs: 15347 / % possible obs: 99.6 % / Redundancy: 5.1 % / Net I/σ(I): 22.4
Reflection shellResolution: 2.6→2.8 Å / Redundancy: 5 % / Rmerge(I) obs: 0.378 / Mean I/σ(I) obs: 4.67 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1GPM

1gpm


Resolution: 2.6→38.972 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 23.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2542 767 5 %
Rwork0.205 --
obs0.2073 15347 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→38.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3575 0 12 93 3680
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023660
X-RAY DIFFRACTIONf_angle_d0.5514958
X-RAY DIFFRACTIONf_dihedral_angle_d10.7931299
X-RAY DIFFRACTIONf_chiral_restr0.023549
X-RAY DIFFRACTIONf_plane_restr0.003638
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5999-2.80060.34781600.27252846X-RAY DIFFRACTION100
2.8006-3.08240.31981530.24692885X-RAY DIFFRACTION100
3.0824-3.52810.29821540.23072898X-RAY DIFFRACTION100
3.5281-4.44410.22931400.18312922X-RAY DIFFRACTION100
4.4441-38.97620.2021600.17793029X-RAY DIFFRACTION99

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