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- PDB-7lvp: Cryptococcus neoformans AIR synthetase -

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Basic information

Entry
Database: PDB / ID: 7lvp
TitleCryptococcus neoformans AIR synthetase
ComponentsAIR synthase
KeywordsBIOSYNTHETIC PROTEIN / LIGASE / AIR synthetase / phosphoribosyl-aminoimidazole synthetase / phosphoribosylaminoimidazole 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
GLYCINE / PHOSPHATE ION / SUCCINIC ACID / Bifunctional purine biosynthetic protein ADE5,7
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 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: AIR synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2398
Polymers35,6701
Non-polymers5697
Water1,11762
1
A: AIR synthase
hetero molecules

A: AIR synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,47816
Polymers71,3392
Non-polymers1,13914
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Buried area3300 Å2
ΔGint-24 kcal/mol
Surface area24390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.300, 85.769, 37.018
Angle α, β, γ (deg.)90.000, 91.698, 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-532-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein AIR synthase / Glycinamide ribonucleotide synthetase / Phosphoribosyl-aminoimidazole synthetase / ...Glycinamide ribonucleotide synthetase / Phosphoribosyl-aminoimidazole synthetase / Phosphoribosylamine--glycine ligase / Phosphoribosylformylglycinamidine cyclo-ligase / Phosphoribosylglycinamide synthetase


Mass: 35669.668 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 69 molecules

#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-SIN / SUCCINIC ACID


Mass: 118.088 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 1.9 Å3/Da / Density % sol: 35.17 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M SPG (succinic acid, sodium dihydrogen phosphate, and glycine in ratio of 2:7:7), 25% w/v PEG1500

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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: Aug 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.24→42.88 Å / Num. obs: 12876 / % possible obs: 99.7 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.95 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rrim(I) all: 0.092 / Net I/σ(I): 0.148
Reflection shellResolution: 2.24→2.31 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.693 / Mean I/σ(I) obs: 0.026 / Num. unique obs: 1148 / CC1/2: 0.848 / Rrim(I) all: 0.823 / % possible all: 96.8

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
Blu-Icedata collection
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Coot0.8.9.2model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5VK4

5vk4


Resolution: 2.24→42.88 Å / SU ML: 0.2399 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 30.9268
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.237 552 4.29 %
Rwork0.1965 12317 -
obs0.1983 12869 99.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.71 Å2
Refinement stepCycle: LAST / Resolution: 2.24→42.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2103 0 35 62 2200
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00172167
X-RAY DIFFRACTIONf_angle_d0.42062930
X-RAY DIFFRACTIONf_chiral_restr0.0415344
X-RAY DIFFRACTIONf_plane_restr0.0027370
X-RAY DIFFRACTIONf_dihedral_angle_d9.6326773
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.24-2.460.30361350.23733036X-RAY DIFFRACTION98.75
2.46-2.820.24441340.2153070X-RAY DIFFRACTION99.94
2.82-3.550.23851340.20843094X-RAY DIFFRACTION99.94
3.55-42.880.22221490.17853117X-RAY DIFFRACTION99.94

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