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- PDB-9k03: Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutan... -

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Basic information

Entry
Database: PDB / ID: 9k03
TitleCrystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to AMPPNP
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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / : / : / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 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 H239A mutant bound to AMPPNP
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)71,75810
Polymers70,4472
Non-polymers1,3108
Water5,423301
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9040 Å2
ΔGint-85 kcal/mol
Surface area22380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.375, 113.038, 70.550
Angle α, β, γ (deg.)90.00, 106.39, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-616-

HOH

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Components

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


Mass: 35223.734 Da / Num. of mol.: 2 / Mutation: H239A
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-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2.63 Å3/Da / Density % sol: 53.32 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: potassium chloride, pentaerythritol ethoxylate, glycine

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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 EIGER X 16M / Detector: PIXEL / Date: Apr 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.25→30 Å / Num. obs: 36341 / % possible obs: 99 % / Redundancy: 4.8 % / Biso Wilson estimate: 29.34 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.134 / Net I/σ(I): 8.99
Reflection shellResolution: 2.25→2.31 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.48 / Num. unique obs: 2758 / CC1/2: 0.724 / % 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
Starting model: 9K00

9k00


Resolution: 2.25→28.26 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2054 1835 5.05 %
Rwork0.1637 --
obs0.1658 36337 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.25→28.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 68 301 5327
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065128
X-RAY DIFFRACTIONf_angle_d0.7426946
X-RAY DIFFRACTIONf_dihedral_angle_d13.588762
X-RAY DIFFRACTIONf_chiral_restr0.049792
X-RAY DIFFRACTIONf_plane_restr0.005876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.310.27871130.20772645X-RAY DIFFRACTION98
2.31-2.380.25891420.19842607X-RAY DIFFRACTION98
2.38-2.460.26091380.19732668X-RAY DIFFRACTION99
2.46-2.550.24551510.18452608X-RAY DIFFRACTION99
2.55-2.650.23171240.18192669X-RAY DIFFRACTION99
2.65-2.770.21991310.16862645X-RAY DIFFRACTION99
2.77-2.920.21571290.16662655X-RAY DIFFRACTION99
2.92-3.10.21581490.15912648X-RAY DIFFRACTION99
3.1-3.340.21061660.15642676X-RAY DIFFRACTION99
3.34-3.670.18951490.14872634X-RAY DIFFRACTION99
3.67-4.20.20121350.14112672X-RAY DIFFRACTION99
4.2-5.290.15761540.14022666X-RAY DIFFRACTION100
5.29-28.260.19451540.18472709X-RAY DIFFRACTION99

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