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- PDB-9k05: Crystal structure of Pyrococcus abyssi AIR synthetase N186A mutan... -

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Basic information

Entry
Database: PDB / ID: 9k05
TitleCrystal structure of Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and 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 / '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 / Chem-FGR / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 Pyrococcus abyssi AIR synthetase N186A mutant bound to FGAR and 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)74,6946
Polymers73,3712
Non-polymers1,3234
Water10,449580
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9090 Å2
ΔGint-60 kcal/mol
Surface area22920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.854, 112.294, 71.343
Angle α, β, γ (deg.)90.000, 106.329, 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-659-

HOH

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Components

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


Mass: 36685.363 Da / Num. of mol.: 2 / Mutation: N186A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus abyssi GE5 (archaea) / Gene: purM, PYRAB16520, PAB1083 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UY56, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical ChemComp-FGR / N-(N-FORMYLGLYCYL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE


Mass: 314.186 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15N2O9P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 2 / 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.: 580 / 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: 2.1 Å3/Da / Density % sol: 41.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: lithium sulfate, poly(acrylic acid sodium salt) 2100, HEPES

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Nov 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 71494 / % possible obs: 99.2 % / Redundancy: 3.5 % / Biso Wilson estimate: 21.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Net I/σ(I): 11.68
Reflection shellResolution: 1.8→1.82 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.577 / Mean I/σ(I) obs: 2 / Num. unique obs: 3520 / CC1/2: 0.695 / % possible all: 94.7

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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: 1.8→28.07 Å / SU ML: 0.2071 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.6064
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1925 3520 4.92 %
Rwork0.1587 67974 -
obs0.1604 71494 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.42 Å2
Refinement stepCycle: LAST / Resolution: 1.8→28.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5162 0 86 580 5828
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00665344
X-RAY DIFFRACTIONf_angle_d0.93677232
X-RAY DIFFRACTIONf_chiral_restr0.0571826
X-RAY DIFFRACTIONf_plane_restr0.007914
X-RAY DIFFRACTIONf_dihedral_angle_d9.6973796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.32141330.31152573X-RAY DIFFRACTION94.71
1.82-1.850.3171360.27092752X-RAY DIFFRACTION99.69
1.85-1.880.27461490.24932713X-RAY DIFFRACTION99.65
1.88-1.910.26531440.22812728X-RAY DIFFRACTION99.58
1.91-1.940.26811390.22742698X-RAY DIFFRACTION99.65
1.94-1.970.25411230.2122719X-RAY DIFFRACTION99.65
1.97-2.010.2761260.20522778X-RAY DIFFRACTION99.69
2.01-2.040.24191640.20222695X-RAY DIFFRACTION99.72
2.04-2.090.23071470.19792700X-RAY DIFFRACTION99.48
2.09-2.130.22881500.19142709X-RAY DIFFRACTION99.72
2.13-2.180.22091540.17382730X-RAY DIFFRACTION99.59
2.18-2.240.22011390.16892734X-RAY DIFFRACTION99.62
2.24-2.30.2311490.16542712X-RAY DIFFRACTION99.65
2.3-2.360.21041340.16652714X-RAY DIFFRACTION99.65
2.36-2.440.20491460.16212727X-RAY DIFFRACTION99.58
2.44-2.530.1951370.16012723X-RAY DIFFRACTION99.34
2.53-2.630.21561530.15972723X-RAY DIFFRACTION99.38
2.63-2.750.20351470.162707X-RAY DIFFRACTION99.06
2.75-2.890.22851270.1662707X-RAY DIFFRACTION99.3
2.89-3.070.18191410.16052735X-RAY DIFFRACTION99.07
3.07-3.310.18111370.14592709X-RAY DIFFRACTION98.17
3.31-3.640.1461370.1292706X-RAY DIFFRACTION98.58
3.64-4.170.12931510.11872705X-RAY DIFFRACTION98.79
4.17-5.250.14971320.11472768X-RAY DIFFRACTION99.86
5.25-28.070.13881250.13642809X-RAY DIFFRACTION99.12

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