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- PDB-9jzx: Crystal structure of E. coli AIR synthetase bound to AMP -

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Basic information

Entry
Database: PDB / ID: 9jzx
TitleCrystal structure of E. coli AIR synthetase bound to AMP
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
ADENOSINE MONOPHOSPHATE / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 bound to AMP
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)149,56617
Polymers147,5644
Non-polymers2,00213
Water6,954386
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
B: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,9579
Polymers73,7822
Non-polymers1,1757
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6950 Å2
ΔGint-105 kcal/mol
Surface area25090 Å2
MethodPISA
2
C: Phosphoribosylformylglycinamidine cyclo-ligase
D: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6098
Polymers73,7822
Non-polymers8286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6530 Å2
ΔGint-105 kcal/mol
Surface area25090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.628, 94.174, 209.927
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.: 10 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 386 / 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: 2.21 Å3/Da / Density % sol: 44.24 %
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: 2.5→30 Å / Num. obs: 49434 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 32.59 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.117 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.601 / Mean I/σ(I) obs: 2.39 / Num. unique obs: 2678 / CC1/2: 0.692 / % 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
Starting model: 9JZW

9jzw


Resolution: 2.5→28.75 Å / SU ML: 0.2567 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.2329
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2446 2535 5.13 %
Rwork0.1869 46897 -
obs0.19 49432 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.24 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9930 0 119 386 10435
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.001810265
X-RAY DIFFRACTIONf_angle_d0.525913967
X-RAY DIFFRACTIONf_chiral_restr0.04181601
X-RAY DIFFRACTIONf_plane_restr0.00361796
X-RAY DIFFRACTIONf_dihedral_angle_d6.9991432
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.550.29211350.24342543X-RAY DIFFRACTION96.44
2.55-2.60.28681320.23892541X-RAY DIFFRACTION99.96
2.6-2.660.30231360.23322593X-RAY DIFFRACTION99.78
2.66-2.720.311360.22822574X-RAY DIFFRACTION99.78
2.72-2.790.28341500.22892580X-RAY DIFFRACTION99.85
2.79-2.870.29011390.22222588X-RAY DIFFRACTION99.63
2.87-2.950.30861540.21752588X-RAY DIFFRACTION99.85
2.95-3.040.31611410.20922585X-RAY DIFFRACTION99.42
3.04-3.150.25321360.19832576X-RAY DIFFRACTION99.6
3.15-3.280.28581330.20642602X-RAY DIFFRACTION99.27
3.28-3.430.24311280.19562610X-RAY DIFFRACTION99.42
3.43-3.610.25181450.18462586X-RAY DIFFRACTION99.38
3.61-3.830.21961720.16952582X-RAY DIFFRACTION99.53
3.83-4.130.2171160.15872626X-RAY DIFFRACTION99.35
4.13-4.540.19441430.13992634X-RAY DIFFRACTION98.9
4.54-5.20.19861650.15272624X-RAY DIFFRACTION99.22
5.2-6.540.22621330.19642691X-RAY DIFFRACTION99.4
6.54-28.750.2181410.16972774X-RAY DIFFRACTION98.18

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