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- PDB-7lvo: Cryptococcus neoformans GAR synthetase -

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Basic information

Entry
Database: PDB / ID: 7lvo
TitleCryptococcus neoformans GAR synthetase
Componentsphosphoribosyl-glycinamide (GAR) synthetase
KeywordsBIOSYNTHETIC PROTEIN / LIGASE / GAR synthetase / phosphoribosyl-glycinamide synthetase / phosphoribosylglycinamide synthetase
Function / homology
Function and homology information


phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase / phosphoribosylamine-glycine ligase activity / purine nucleobase biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / metal ion binding / cytosol
Similarity search - Function
Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain ...Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase / Phosphoribosylglycinamide synthetase, conserved site / Phosphoribosylglycinamide synthetase, C-domain / Phosphoribosylglycinamide synthetase, N-terminal / Phosphoribosylglycinamide synthetase, C-domain superfamily / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, N domain / Phosphoribosylglycinamide synthetase signature. / Phosphoribosylglycinamide synthetase, C domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / Phosphoribosylglycinamide synthetase, ATP-grasp (A) domain / PurM-like, N-terminal domain / AIR synthase related protein, N-terminal domain / PurM-like, C-terminal domain / PurM-like, C-terminal domain superfamily / PurM-like, N-terminal domain superfamily / AIR synthase related protein, C-terminal domain / Rudiment single hybrid motif / ATP-grasp fold, subdomain 1 / Pre-ATP-grasp domain superfamily / ATP-grasp fold / ATP-grasp fold profile.
Similarity search - Domain/homology
Bifunctional purine biosynthetic protein ADE5,7
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsChua, S.M.H. / Luo, Z. / Lim, B.Y.J. / Kobe, B. / Fraser, J.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Structural features of Cryptococcus neoformans bifunctional GAR/AIR synthetase may present novel antifungal drug targets.
Authors: Chua, S.M.H. / Wizrah, M.S.I. / Luo, Z. / Lim, B.Y.J. / Kappler, U. / Kobe, B. / Fraser, J.A.
History
DepositionFeb 26, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 1, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 29, 2021Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Oct 18, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: phosphoribosyl-glycinamide (GAR) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9574
Polymers50,7711
Non-polymers1863
Water1,856103
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering, 80% monomeric population, 20% dimeric population
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint5 kcal/mol
Surface area18650 Å2
Unit cell
Length a, b, c (Å)87.104, 76.489, 74.968
Angle α, β, γ (deg.)90.000, 107.569, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-608-

HOH

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Components

#1: Protein phosphoribosyl-glycinamide (GAR) synthetase / Glycinamide ribonucleotide synthetase / Phosphoribosyl-aminoimidazole synthetase / ...Glycinamide ribonucleotide synthetase / Phosphoribosyl-aminoimidazole synthetase / Phosphoribosylamine--glycine ligase / Phosphoribosylformylglycinamidine cyclo-ligase


Mass: 50770.594 Da / Num. of mol.: 1 / Fragment: N-terminal half, GAR synthetase function
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_06314
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: J9VYP5, phosphoribosylformylglycinamidine cyclo-ligase, phosphoribosylamine-glycine ligase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.57 Å3/Da / Density % sol: 52.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M sodium citrate, pH 5.0, 30% v/v MPEG550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2→41.52 Å / Num. obs: 31460 / % possible obs: 99 % / Redundancy: 3.4 % / Biso Wilson estimate: 30.26 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Rrim(I) all: 0.067 / Net I/σ(I): 12.4
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.349 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 7982 / CC1/2: 0.874 / Rrim(I) all: 0.479 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Coot1.13-2998model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2QK4

2qk4


Resolution: 2→38.24 Å / SU ML: 0.3001 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.9337
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2855 3164 10.22 %
Rwork0.2416 27810 -
obs0.246 30974 97.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.66 Å2
Refinement stepCycle: LAST / Resolution: 2→38.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3254 0 12 103 3369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00353331
X-RAY DIFFRACTIONf_angle_d0.50614513
X-RAY DIFFRACTIONf_chiral_restr0.0427508
X-RAY DIFFRACTIONf_plane_restr0.0038592
X-RAY DIFFRACTIONf_dihedral_angle_d9.52751227
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.32251400.30921230X-RAY DIFFRACTION99.71
2.03-2.060.31561470.29071218X-RAY DIFFRACTION99.13
2.06-2.10.35431310.28461223X-RAY DIFFRACTION98.83
2.1-2.130.30241330.26511238X-RAY DIFFRACTION99.42
2.13-2.170.29291330.26851199X-RAY DIFFRACTION98.89
2.17-2.210.32621190.26871260X-RAY DIFFRACTION99.14
2.21-2.260.31361400.28221206X-RAY DIFFRACTION98.97
2.26-2.310.35931540.26061216X-RAY DIFFRACTION98.07
2.31-2.360.29051460.25341194X-RAY DIFFRACTION98.75
2.36-2.420.28131700.24671209X-RAY DIFFRACTION98.36
2.42-2.480.29971340.25521193X-RAY DIFFRACTION97.22
2.48-2.560.33971220.25961224X-RAY DIFFRACTION97.54
2.56-2.640.28221440.27211204X-RAY DIFFRACTION97.89
2.64-2.730.29431320.2591222X-RAY DIFFRACTION97.69
2.73-2.840.34021430.25771188X-RAY DIFFRACTION96.94
2.84-2.970.33181450.26781203X-RAY DIFFRACTION97.61
2.97-3.130.28011260.26531200X-RAY DIFFRACTION96.65
3.13-3.330.31221250.26641216X-RAY DIFFRACTION96.34
3.33-3.580.31141400.22591175X-RAY DIFFRACTION94.81
3.58-3.940.27311180.22891194X-RAY DIFFRACTION94.66
3.94-4.510.23781220.19851200X-RAY DIFFRACTION94.97
4.51-5.680.21191620.19591196X-RAY DIFFRACTION96.72
5.69-38.240.27081380.22431202X-RAY DIFFRACTION93.71

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