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- PDB-9k01: Crystal structure of Pyrococcus abyssi AIR synthetase bound to ADP -

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Basic information

Entry
Database: PDB / ID: 9k01
TitleCrystal structure of Pyrococcus abyssi AIR synthetase bound to ADP
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: 1.6 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
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,6286
Polymers70,5822
Non-polymers1,0474
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8150 Å2
ΔGint-96 kcal/mol
Surface area22520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.017, 111.987, 71.119
Angle α, β, γ (deg.)90.000, 106.742, 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
11B-619-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 2.69 Å3/Da / Density % sol: 54.3 %
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: May 2, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.6→30 Å / Num. obs: 103545 / % possible obs: 99.9 % / Redundancy: 6.8 % / Biso Wilson estimate: 23.34 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.043 / Net I/σ(I): 22.24
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.706 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3360 / CC1/2: 0.808 / % possible all: 98.4

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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: 1.6→29.09 Å / SU ML: 0.1693 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.8626
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1927 5137 4.96 %
Rwork0.1656 98408 -
obs0.167 103545 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 29.58 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4968 0 64 240 5272
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00675153
X-RAY DIFFRACTIONf_angle_d0.96176981
X-RAY DIFFRACTIONf_chiral_restr0.0605793
X-RAY DIFFRACTIONf_plane_restr0.0071881
X-RAY DIFFRACTIONf_dihedral_angle_d10.6972723
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.3141710.28863189X-RAY DIFFRACTION98.36
1.62-1.640.26461800.24413306X-RAY DIFFRACTION99.97
1.64-1.660.23871630.22593250X-RAY DIFFRACTION100
1.66-1.680.27471780.21713289X-RAY DIFFRACTION100
1.68-1.70.24811680.21213255X-RAY DIFFRACTION99.97
1.7-1.730.2411730.21363264X-RAY DIFFRACTION100
1.73-1.750.23741730.20723275X-RAY DIFFRACTION100
1.75-1.780.25931840.21213278X-RAY DIFFRACTION99.97
1.78-1.810.25551840.21223251X-RAY DIFFRACTION99.97
1.81-1.840.22221620.19633295X-RAY DIFFRACTION100
1.84-1.870.24981770.193270X-RAY DIFFRACTION100
1.87-1.90.20291860.18133247X-RAY DIFFRACTION100
1.9-1.940.23071780.1843274X-RAY DIFFRACTION99.97
1.94-1.980.1981570.17733306X-RAY DIFFRACTION100
1.98-2.020.20091680.17493258X-RAY DIFFRACTION99.94
2.02-2.070.21361580.17773281X-RAY DIFFRACTION100
2.07-2.120.2251660.17543301X-RAY DIFFRACTION99.97
2.12-2.180.20871570.17213289X-RAY DIFFRACTION99.94
2.18-2.240.18131650.16263301X-RAY DIFFRACTION100
2.24-2.310.19951620.16743268X-RAY DIFFRACTION100
2.31-2.40.18951600.17453302X-RAY DIFFRACTION100
2.4-2.490.20471720.17533304X-RAY DIFFRACTION99.94
2.49-2.610.20171800.17143272X-RAY DIFFRACTION99.86
2.61-2.740.20051840.16573277X-RAY DIFFRACTION100
2.74-2.910.19241780.16453247X-RAY DIFFRACTION99.91
2.91-3.140.17571670.15693309X-RAY DIFFRACTION99.83
3.14-3.450.15721710.14663286X-RAY DIFFRACTION99.88
3.45-3.950.16311700.13513307X-RAY DIFFRACTION99.86
3.95-4.980.14951740.13313317X-RAY DIFFRACTION99.89
4.98-29.090.20891710.17283340X-RAY DIFFRACTION99.24

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