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- PDB-9k04: Crystal structure of Pyrococcus abyssi AIR synthetase H239A mutan... -

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Basic information

Entry
Database: PDB / ID: 9k04
TitleCrystal structure of Pyrococcus abyssi AIR synthetase H239A mutant bound to ADP and Pi
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 / : / : / PHOSPHATE ION / 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 H239A mutant bound to ADP and Pi
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)71,86814
Polymers70,4472
Non-polymers1,42012
Water10,359575
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-115 kcal/mol
Surface area22100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.964, 112.216, 70.512
Angle α, β, γ (deg.)90.000, 105.817, 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

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Protein , 1 types, 2 molecules AB

#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

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Non-polymers , 5 types, 587 molecules

#2: 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
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 575 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.68 Å3/Da / Density % sol: 54.18 %
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 EIGER2 X 16M / Detector: PIXEL / Date: Apr 24, 2025
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: 99620 / % possible obs: 99.2 % / Redundancy: 6.9 % / Biso Wilson estimate: 16.78 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.062 / Net I/σ(I): 19.17
Reflection shellResolution: 1.6→1.62 Å / Redundancy: 7 % / Rmerge(I) obs: 0.777 / Mean I/σ(I) obs: 2.87 / Num. unique obs: 3248 / CC1/2: 0.782 / % possible all: 97.4

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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: 1.6→26.93 Å / SU ML: 0.1597 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.63
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1767 5142 5.16 %
Rwork0.1567 94477 -
obs0.1578 99619 99.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 21.92 Å2
Refinement stepCycle: LAST / Resolution: 1.6→26.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4958 0 72 575 5605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00685152
X-RAY DIFFRACTIONf_angle_d1.0556980
X-RAY DIFFRACTIONf_chiral_restr0.0631794
X-RAY DIFFRACTIONf_plane_restr0.01882
X-RAY DIFFRACTIONf_dihedral_angle_d12.6596724
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.620.26991910.22843057X-RAY DIFFRACTION97.36
1.62-1.640.24021600.21543117X-RAY DIFFRACTION98.2
1.64-1.660.21651660.213125X-RAY DIFFRACTION98.68
1.66-1.680.24661570.20023116X-RAY DIFFRACTION98.26
1.68-1.710.22641540.19893137X-RAY DIFFRACTION98.86
1.71-1.730.26631500.20693162X-RAY DIFFRACTION98.57
1.73-1.750.24431880.20043083X-RAY DIFFRACTION98.82
1.75-1.780.23881660.18523117X-RAY DIFFRACTION98.86
1.78-1.810.20861870.1783145X-RAY DIFFRACTION98.78
1.81-1.840.18491790.1663104X-RAY DIFFRACTION99.03
1.84-1.870.19451800.16193150X-RAY DIFFRACTION99.02
1.87-1.90.20411740.15583150X-RAY DIFFRACTION99.05
1.9-1.940.18171870.15163075X-RAY DIFFRACTION99.18
1.94-1.980.19151840.15533141X-RAY DIFFRACTION99.31
1.98-2.020.16671770.15513138X-RAY DIFFRACTION99.22
2.02-2.070.19261590.15663166X-RAY DIFFRACTION99.31
2.07-2.120.17841900.14633135X-RAY DIFFRACTION99.4
2.12-2.180.16731680.14333174X-RAY DIFFRACTION99.55
2.18-2.240.18771600.14843167X-RAY DIFFRACTION99.61
2.24-2.310.18811410.1563160X-RAY DIFFRACTION99.52
2.31-2.40.15691680.15213199X-RAY DIFFRACTION99.62
2.4-2.490.18371660.15383147X-RAY DIFFRACTION99.73
2.49-2.610.16471720.15383183X-RAY DIFFRACTION99.7
2.61-2.740.15941530.15553178X-RAY DIFFRACTION99.82
2.74-2.910.18251580.15443186X-RAY DIFFRACTION99.88
2.91-3.140.16891860.15393171X-RAY DIFFRACTION99.97
3.14-3.450.16381900.15233177X-RAY DIFFRACTION99.91
3.46-3.950.14911750.1383173X-RAY DIFFRACTION99.94
3.95-4.980.14161740.12823204X-RAY DIFFRACTION99.97
4.98-26.930.17711820.17523240X-RAY DIFFRACTION99.8

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