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- PDB-9jzy: Crystal structure of Pyrococcus horikoshii AIR synthetase -

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Basic information

Entry
Database: PDB / ID: 9jzy
TitleCrystal structure of Pyrococcus horikoshii 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 / '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 speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.26 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 horikoshii 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

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,68613
Polymers36,9611
Non-polymers72512
Water1,72996
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules

A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)75,37226
Polymers73,9222
Non-polymers1,45024
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area8200 Å2
ΔGint-566 kcal/mol
Surface area24870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.022, 56.022, 198.990
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-575-

HOH

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Components

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


Mass: 36960.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus horikoshii OT3 (archaea) / Gene: purM, PH0316 / Production host: Escherichia coli (E. coli)
References: UniProt: O58054, phosphoribosylformylglycinamidine cyclo-ligase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.65 Å3/Da / Density % sol: 53.57 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: zinc acetate, 2-propanol, sodium cacodylate

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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 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.26→30 Å / Num. obs: 15440 / % possible obs: 98.4 % / Redundancy: 12.3 % / Biso Wilson estimate: 36.64 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Net I/σ(I): 20.57
Reflection shellResolution: 2.26→2.4 Å / Redundancy: 13.2 % / Rmerge(I) obs: 0.175 / Mean I/σ(I) obs: 10.48 / Num. unique obs: 2488 / CC1/2: 0.993 / % possible all: 97.8

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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: in-house SAD model

Resolution: 2.26→28.54 Å / SU ML: 0.2531 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0968
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2676 792 5.13 %
Rwork0.2072 14648 -
obs0.2101 15440 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.87 Å2
Refinement stepCycle: LAST / Resolution: 2.26→28.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2458 0 12 96 2566
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032501
X-RAY DIFFRACTIONf_angle_d0.6043378
X-RAY DIFFRACTIONf_chiral_restr0.0461390
X-RAY DIFFRACTIONf_plane_restr0.0038427
X-RAY DIFFRACTIONf_dihedral_angle_d5.3477335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.40.32691470.23432341X-RAY DIFFRACTION97.8
2.4-2.590.28271270.22812359X-RAY DIFFRACTION98.3
2.59-2.850.28751260.23862405X-RAY DIFFRACTION98.1
2.85-3.260.29721280.2262416X-RAY DIFFRACTION98.26
3.26-4.10.27991380.20052457X-RAY DIFFRACTION98.74
4.1-28.540.21971260.18572670X-RAY DIFFRACTION99.15

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