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- PDB-9k06: Crystal structure of Pyrococcus abyssi AIR synthetase with residu... -

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Basic information

Entry
Database: PDB / ID: 9k06
TitleCrystal structure of Pyrococcus abyssi AIR synthetase with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56
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
CITRATE ANION / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesPyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 with residues 51-54 replaced by Neisseria gonorrhoeae residues 49-56
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)72,0836
Polymers71,5132
Non-polymers5704
Water5,855325
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-69 kcal/mol
Surface area23460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.905, 112.790, 70.906
Angle α, β, γ (deg.)90.000, 107.074, 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: 35756.387 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-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 325 / 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: 2.92 Å3/Da / Density % sol: 57.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: lithium sulfate, 2-propanol, sodium citrate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Sep 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 86257 / % possible obs: 99.4 % / Redundancy: 3.5 % / Biso Wilson estimate: 51.35 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Net I/σ(I): 12.44
Reflection shellResolution: 1.7→1.72 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.455 / Mean I/σ(I) obs: 2.49 / Num. unique obs: 4466 / CC1/2: 0.784 / % possible all: 95.5

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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: 1.7→28.61 Å / SU ML: 0.1807 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.3914
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1958 4466 5.18 %
Rwork0.1677 81791 -
obs0.1692 86257 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.76 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5032 0 36 325 5393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685154
X-RAY DIFFRACTIONf_angle_d0.92566968
X-RAY DIFFRACTIONf_chiral_restr0.0606790
X-RAY DIFFRACTIONf_plane_restr0.0072890
X-RAY DIFFRACTIONf_dihedral_angle_d6.6752716
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.720.29341570.26312618X-RAY DIFFRACTION95.46
1.72-1.740.29781470.23792744X-RAY DIFFRACTION99.79
1.74-1.760.25271390.21522715X-RAY DIFFRACTION99.83
1.76-1.780.21841580.20152718X-RAY DIFFRACTION99.72
1.78-1.80.22691460.20082736X-RAY DIFFRACTION99.83
1.8-1.830.2161490.19632722X-RAY DIFFRACTION99.72
1.83-1.860.25231680.20932668X-RAY DIFFRACTION99.82
1.86-1.880.26811530.20892764X-RAY DIFFRACTION99.79
1.88-1.910.21871530.19792726X-RAY DIFFRACTION99.65
1.91-1.940.24091580.19432698X-RAY DIFFRACTION99.69
1.94-1.980.21191730.18482736X-RAY DIFFRACTION99.66
1.98-2.010.21491480.17572711X-RAY DIFFRACTION99.69
2.01-2.050.23361340.17082742X-RAY DIFFRACTION99.65
2.05-2.090.21281540.16742719X-RAY DIFFRACTION99.69
2.09-2.140.21031610.16892724X-RAY DIFFRACTION99.48
2.14-2.190.18351270.17032715X-RAY DIFFRACTION99.58
2.19-2.240.19231420.17292727X-RAY DIFFRACTION99.48
2.24-2.30.21031250.1742776X-RAY DIFFRACTION99.69
2.3-2.370.2141470.17152709X-RAY DIFFRACTION99.55
2.37-2.450.19061440.17122736X-RAY DIFFRACTION99.11
2.45-2.540.20651510.17772742X-RAY DIFFRACTION99.52
2.54-2.640.22011310.17142712X-RAY DIFFRACTION99.37
2.64-2.760.21641340.17472779X-RAY DIFFRACTION99.52
2.76-2.90.23471430.17372703X-RAY DIFFRACTION99.34
2.9-3.080.20031570.18452766X-RAY DIFFRACTION99.56
3.08-3.320.16591560.1642689X-RAY DIFFRACTION99.13
3.32-3.660.18791680.14632707X-RAY DIFFRACTION99.34
3.66-4.180.14041360.13262765X-RAY DIFFRACTION99.28
4.18-5.270.15861590.13582733X-RAY DIFFRACTION99.21
5.27-28.610.18961480.17272791X-RAY DIFFRACTION98.96

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