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- PDB-4wim: Crystal Structure of the GMP Synthetase from Plasmodium falciparum -

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Basic information

Entry
Database: PDB / ID: 4wim
TitleCrystal Structure of the GMP Synthetase from Plasmodium falciparum
ComponentsGMP synthetase
KeywordsLYASE / GMP synthetase / purine salvage pathway
Function / homology
Function and homology information


Purine ribonucleoside monophosphate biosynthesis / GMP synthase (glutamine-hydrolyzing) activity / Azathioprine ADME / GMP synthase 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 / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / 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 / GMP Synthetase; Chain A, domain 3 - #10 / NAD/GMP synthase / NAD synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase / 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
GMP synthase [glutamine-hydrolyzing]
Similarity search - Component
Biological speciesPlasmodium falciparum 3D7 (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 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 2.0Oct 24, 2018Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Source and taxonomy
Category: atom_site / entity_src_gen ...atom_site / entity_src_gen / pdbx_nonpoly_scheme / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_scientific_name / _pdbx_nonpoly_scheme.auth_seq_num
Revision 2.1Jan 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


Theoretical massNumber of molelcules
Total (without water)130,9752
Polymers130,9752
Non-polymers00
Water41423
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-15 kcal/mol
Surface area50670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.453, 68.548, 102.080
Angle α, β, γ (deg.)101.11, 99.17, 93.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein GMP synthetase


Mass: 65487.609 Da / Num. of mol.: 2 / Fragment: UNP residues 2-554
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum 3D7 (eukaryote) / Gene: PF10_0123 / Plasmid: pQE30 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8IJR9, GMP synthase (glutamine-hydrolysing)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / 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: 2.24 Å3/Da / Density % sol: 45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 20% (w/v) PEG 3350, 0.2 M Diammonium tartrate and 5 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97239 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97239 Å / Relative weight: 1
ReflectionResolution: 3.6→98.6 Å / Num. obs: 13123 / % possible obs: 88.8 % / Redundancy: 1.7 % / Net I/σ(I): 7.2
Reflection shellResolution: 3.6→3.96 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 1.34 / % possible all: 84

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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: 3UOW

3uow


Resolution: 3.6→49.305 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 37.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2927 594 5.06 %
Rwork0.2815 --
obs0.2821 11730 89.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.305 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7281 0 0 23 7304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0357411
X-RAY DIFFRACTIONf_angle_d3.44810084
X-RAY DIFFRACTIONf_dihedral_angle_d19.1672527
X-RAY DIFFRACTIONf_chiral_restr0.231179
X-RAY DIFFRACTIONf_plane_restr0.0151314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.96220.33071580.30672855X-RAY DIFFRACTION92
3.9622-4.53520.35611600.26992759X-RAY DIFFRACTION90
4.5352-5.71250.29071330.27982809X-RAY DIFFRACTION89
5.7125-49.30990.26251430.27942713X-RAY DIFFRACTION87

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