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- PDB-9jzw: Crystal structure of E. coli AIR synthetase -

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Basic information

Entry
Database: PDB / ID: 9jzw
TitleCrystal structure of E. coli AIR synthetase
ComponentsPhosphoribosylformylglycinamidine cyclo-ligase
KeywordsLIGASE / Purine synthesis / ATP hydrolysis
Function / homology
Function and homology information


adenine biosynthetic process / phosphoribosylformylglycinamidine cyclo-ligase / phosphoribosylformylglycinamidine cyclo-ligase activity / phosphoribosylamine-glycine ligase activity / purine nucleotide biosynthetic process / 'de novo' IMP biosynthetic process / ATP binding / cytosol
Similarity search - Function
Phosphoribosylformylglycinamidine cyclo-ligase / 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
Similarity search - Domain/homology
Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsChen, Y.H. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: To Be Published
Title: Crystal structure of E. coli AIR synthetase
Authors: Chen, Y.H. / Chen, C.J.
History
DepositionOct 15, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
C: Phosphoribosylformylglycinamidine cyclo-ligase
D: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)148,42813
Polymers147,5644
Non-polymers8659
Water10,215567
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1666
Polymers73,7822
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-100 kcal/mol
Surface area25470 Å2
MethodPISA
2
C: Phosphoribosylformylglycinamidine cyclo-ligase
D: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,2627
Polymers73,7822
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-107 kcal/mol
Surface area25500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.697, 94.408, 211.056
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Phosphoribosylformylglycinamidine cyclo-ligase / AIR synthase / AIRS / Phosphoribosyl-aminoimidazole synthetase


Mass: 36890.941 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: purM, purG, b2499, JW2484 / Production host: Escherichia coli (E. coli)
References: UniProt: P08178, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 567 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.23 Å3/Da / Density % sol: 44.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: ammonium sulfate, 2-propanol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. obs: 82539 / % possible obs: 98.4 % / Redundancy: 6.7 % / Biso Wilson estimate: 25.37 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.7
Reflection shellResolution: 2.1→2.13 Å / Redundancy: 2.89 % / Rmerge(I) obs: 0.72 / Mean I/σ(I) obs: 2.89 / Num. unique obs: 2711 / CC1/2: 0.755 / % possible all: 96.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSv20200131data reduction
XDSv20200131data scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→25.36 Å / SU ML: 0.2332 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.2322
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2391 4129 5 %
Rwork0.1981 78404 -
obs0.2002 82533 98.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.92 Å2
Refinement stepCycle: LAST / Resolution: 2.1→25.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9903 0 45 567 10515
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001910157
X-RAY DIFFRACTIONf_angle_d0.506213807
X-RAY DIFFRACTIONf_chiral_restr0.04291586
X-RAY DIFFRACTIONf_plane_restr0.00351787
X-RAY DIFFRACTIONf_dihedral_angle_d4.71721400
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.31951410.25252570X-RAY DIFFRACTION96.41
2.13-2.150.35961170.23552690X-RAY DIFFRACTION97.3
2.15-2.180.25791580.22992614X-RAY DIFFRACTION97.43
2.18-2.210.28421230.21792663X-RAY DIFFRACTION98.65
2.21-2.240.3121310.22412660X-RAY DIFFRACTION96.51
2.24-2.270.26081370.22692663X-RAY DIFFRACTION98.94
2.27-2.310.24691390.22212649X-RAY DIFFRACTION96.91
2.31-2.340.27991350.22722685X-RAY DIFFRACTION99.16
2.34-2.380.27391570.22062637X-RAY DIFFRACTION97.35
2.38-2.420.29821510.21642716X-RAY DIFFRACTION98.86
2.42-2.470.26781490.21132617X-RAY DIFFRACTION97.36
2.47-2.510.23921490.22542661X-RAY DIFFRACTION99.22
2.51-2.570.27251390.21872710X-RAY DIFFRACTION97.34
2.57-2.620.27491470.21842699X-RAY DIFFRACTION99.68
2.62-2.680.26251360.21822660X-RAY DIFFRACTION97.83
2.68-2.750.27661100.2112742X-RAY DIFFRACTION98.72
2.75-2.820.25061290.21362740X-RAY DIFFRACTION99.31
2.82-2.910.25721400.21412665X-RAY DIFFRACTION98.21
2.91-30.27551370.21082719X-RAY DIFFRACTION98.55
3-3.110.29031630.21352719X-RAY DIFFRACTION99.17
3.11-3.230.22981500.20162705X-RAY DIFFRACTION98.55
3.23-3.380.24231520.20332701X-RAY DIFFRACTION98.41
3.38-3.560.22751410.19662714X-RAY DIFFRACTION98.69
3.56-3.780.23441360.17962761X-RAY DIFFRACTION98.57
3.78-4.070.23251560.17332727X-RAY DIFFRACTION99.21
4.07-4.480.18361480.15452779X-RAY DIFFRACTION99.12
4.48-5.120.16441460.1582784X-RAY DIFFRACTION99.32
5.12-6.440.22031500.19772822X-RAY DIFFRACTION99.56
6.44-25.360.19161620.17872932X-RAY DIFFRACTION98.5

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