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- PDB-9k02: Crystal structure of Pyrococcus abyssi AIR synthetase bound to AD... -

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Basic information

Entry
Database: PDB / ID: 9k02
TitleCrystal structure of Pyrococcus abyssi AIR synthetase bound to ADP and Mg(II)
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-5'-DIPHOSPHATE / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 bound to ADP and Mg(II)
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)71,72510
Polymers70,5822
Non-polymers1,1448
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8630 Å2
ΔGint-146 kcal/mol
Surface area22510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.430, 112.532, 71.532
Angle α, β, γ (deg.)90.000, 106.437, 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

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Components

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


Mass: 35290.805 Da / Num. of mol.: 2
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.7 Å3/Da / Density % sol: 54.36 %
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 07A / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 52121 / % possible obs: 96.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 28.84 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Net I/σ(I): 14.22
Reflection shellResolution: 2→2.03 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.468 / Mean I/σ(I) obs: 2.47 / Num. unique obs: 2646 / CC1/2: 0.787 / % possible all: 93.7

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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: 2→28.95 Å / SU ML: 0.2243 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.3987
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2067 2617 5.02 %
Rwork0.1642 49504 -
obs0.1663 52121 96.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.78 Å2
Refinement stepCycle: LAST / Resolution: 2→28.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 68 565 5601
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00785140
X-RAY DIFFRACTIONf_angle_d1.05066960
X-RAY DIFFRACTIONf_chiral_restr0.0609792
X-RAY DIFFRACTIONf_plane_restr0.0095878
X-RAY DIFFRACTIONf_dihedral_angle_d10.6905720
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.030.30631220.25422524X-RAY DIFFRACTION93.66
2.03-2.070.25441240.23012583X-RAY DIFFRACTION96.78
2.07-2.110.29531360.22112599X-RAY DIFFRACTION96.34
2.11-2.160.26741390.20422584X-RAY DIFFRACTION96.59
2.16-2.210.26641250.19312585X-RAY DIFFRACTION97.27
2.21-2.270.26831360.20142630X-RAY DIFFRACTION97.02
2.27-2.330.25491270.20052629X-RAY DIFFRACTION96.84
2.33-2.40.2481380.19642592X-RAY DIFFRACTION96.74
2.4-2.470.25321460.19682590X-RAY DIFFRACTION97.02
2.47-2.560.26641440.19372601X-RAY DIFFRACTION97.1
2.56-2.660.24711420.19232573X-RAY DIFFRACTION97.1
2.66-2.780.28611430.18042608X-RAY DIFFRACTION97.52
2.78-2.930.22711260.18642626X-RAY DIFFRACTION97.24
2.93-3.110.24361460.17732596X-RAY DIFFRACTION96.65
3.11-3.350.20581560.15812623X-RAY DIFFRACTION98.09
3.35-3.690.17261530.14712616X-RAY DIFFRACTION97.71
3.69-4.220.14961430.12142618X-RAY DIFFRACTION97.08
4.22-5.320.13541340.11832638X-RAY DIFFRACTION97.54
5.32-28.950.15941370.1422689X-RAY DIFFRACTION97.41

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