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- PDB-9jzz: Crystal structure of Pyrococcus horikoshii AIR synthetase bound to AMP -

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Basic information

Entry
Database: PDB / ID: 9jzz
TitleCrystal structure of Pyrococcus horikoshii 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 / '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 speciesPyrococcus horikoshii OT3 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 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

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Assembly

Deposited unit
A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,03314
Polymers36,9611
Non-polymers1,07213
Water84747
1
A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules

A: Phosphoribosylformylglycinamidine cyclo-ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,06628
Polymers73,9222
Non-polymers2,14426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area9450 Å2
ΔGint-590 kcal/mol
Surface area24280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.966, 55.966, 198.814
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-504-

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-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
#3: Chemical
ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 47 / 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: 2.72 Å3/Da / Density % sol: 54.72 %
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: Dec 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.05→30 Å / Num. obs: 20693 / % possible obs: 99.9 % / Redundancy: 8.2 % / Biso Wilson estimate: 36.49 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Net I/σ(I): 19.62
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 3.35 / Num. unique obs: 2877 / CC1/2: 0.89 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDS6.3.3.1data reduction
XDS6.3.3.1data scaling
PHENIX1.21.2_5419phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9JZY

9jzy


Resolution: 2.05→28.05 Å / SU ML: 0.2213 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.0662
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2573 1046 5.05 %
Rwork0.223 19647 -
obs0.2248 20693 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.04 Å2
Refinement stepCycle: LAST / Resolution: 2.05→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2470 0 35 47 2552
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212539
X-RAY DIFFRACTIONf_angle_d0.56133434
X-RAY DIFFRACTIONf_chiral_restr0.0439395
X-RAY DIFFRACTIONf_plane_restr0.0032430
X-RAY DIFFRACTIONf_dihedral_angle_d7.5246346
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.160.32191280.25872749X-RAY DIFFRACTION99.41
2.16-2.30.23921330.24422725X-RAY DIFFRACTION100
2.3-2.470.28081460.24962766X-RAY DIFFRACTION100
2.47-2.720.30131480.26112774X-RAY DIFFRACTION99.97
2.72-3.120.30931620.24732785X-RAY DIFFRACTION100
3.12-3.920.27471580.21662828X-RAY DIFFRACTION100
3.92-28.050.21151710.19633020X-RAY DIFFRACTION99.91

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