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- PDB-9vnv: Crystal structure of Pyrococcus abyssi AIR synthetase with an N-t... -

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Basic information

Entry
Database: PDB / ID: 9vnv
TitleCrystal structure of Pyrococcus abyssi AIR synthetase with an N-terminal 43-residues deletion
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 abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsChen, Y.H. / Chen, C.J.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
National Science Council (NSC, Taiwan) Taiwan
CitationJournal: Int.J.Biol.Macromol. / Year: 2026
Title: Structural insights into substrate binding, domain swapping and heat resistance of a hyperthermostable archaeal AIR synthetase.
Authors: Chen, Y.H. / Huang, Y.C. / Rao, R.G.R. / Chang, H.C. / Lan, Y.H. / Nakagawa, A. / Jeyaraman, J. / Chen, C.J.
History
DepositionJul 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2026Provider: 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)64,1144
Polymers63,9222
Non-polymers1922
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-65 kcal/mol
Surface area22110 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.351, 97.325, 124.228
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
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: 31960.924 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.38 Å3/Da / Density % sol: 48.34 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop
Details: sodium thiocyanate, pentaerythritol propoxylate (5/4 PO/OH), HEPES

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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: Sep 18, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 21814 / % possible obs: 99.7 % / Redundancy: 6.4 % / Biso Wilson estimate: 44.46 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.091 / Net I/σ(I): 15.12
Reflection shellResolution: 2.5→2.63 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.609 / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3202 / CC1/2: 0.806 / % possible all: 98.6

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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: 2.5→29.59 Å / SU ML: 0.3142 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.6744
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 1040 4.77 %
Rwork0.1882 20774 -
obs0.1907 21814 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.91 Å2
Refinement stepCycle: LAST / Resolution: 2.5→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 10 108 4618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00184594
X-RAY DIFFRACTIONf_angle_d0.41566220
X-RAY DIFFRACTIONf_chiral_restr0.0424710
X-RAY DIFFRACTIONf_plane_restr0.0031792
X-RAY DIFFRACTIONf_dihedral_angle_d3.9432626
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.630.30331460.24322892X-RAY DIFFRACTION98.64
2.63-2.790.30831430.22082930X-RAY DIFFRACTION100
2.79-3.010.27711390.21032911X-RAY DIFFRACTION99.97
3.01-3.310.27231500.19432951X-RAY DIFFRACTION99.9
3.31-3.790.21621530.17382956X-RAY DIFFRACTION99.94
3.79-4.770.22171530.15993000X-RAY DIFFRACTION99.97
4.77-29.590.22131560.19493134X-RAY DIFFRACTION99.61
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
15.773600277523.350663606851.900917147974.825349355491.027689596137.36023678821-0.4562143832060.1415565821111.37642922995-0.2603143822910.1598569884450.945640541732-0.369022876962-0.2317519734860.1431688511080.3325852579530.0270163084158-0.1456443857650.534029327258-0.0472969351720.421671914784-7.08437602503-2.03394833151-0.327564888989
27.052763107741.07199767491-0.555813349722.908674388671.209738862192.51317228664-0.07824988061590.01729147286360.101901507304-0.2187115427520.205720376714-0.189626061813-0.2819123281390.378226382618-0.1663253897280.316358315171-0.007523771139750.02233210887870.37152849994-0.006243302611290.27082323841510.66824229420.3498472390128.20851325603
34.335215712770.609368701933-3.411145412143.335098402930.09312931969235.39820029286-0.220886993997-1.93845882881-1.314303012510.278986511543-0.115867913102-0.3027978938350.2602521613360.9683515986320.1831813562960.3900194833850.0335572274146-0.1372909427350.4878401785730.009381315079020.40077426141814.8006926373-7.3009455608213.1566488232
48.147389354223.16076032975-3.894510212235.97454147399-1.241484616195.28756374825-0.2084978157810.0609268314653-0.64376950359-0.60520989685-0.19728085745-0.7581241094010.03702411401020.7327508750520.3384229598620.342761841950.0331872068583-0.03416970387920.4593611583450.033046592080.30747202412916.2018266664-2.955531491350.104504300519
51.89047897863-0.137815313886-0.8750561303931.466393996830.5785566649163.32312925358-0.378862640692-0.1559899765390.455909880858-0.1713985899770.1100643983010.253535777804-0.160327269191-0.01155938677570.201022551780.2980365716760.0230388204931-0.06243603211540.291813241441-0.03374480985330.370232251025-9.004037367362.255660615916.65297050265
66.069389787652.04097256797-0.2086834755583.07458408291.279094532612.857798404120.0763423086517-0.5815477031450.439622459238-0.05099056169130.04551883248490.148928631396-0.1629180647370.426312319664-0.04249334161030.316848591684-0.03218289506910.03658663700820.356998283761-0.03316472270820.2953854547266.213812870569.4220454536317.772011695
75.29009325831-0.6842060553271.906910845892.68362861446-1.718690884463.31702986204-0.3341444074760.5978752546221.11619132263-0.7900864857440.2465837242280.881202597797-0.0539093524513-0.01000200220710.0005263039881610.464722600821-0.0182689796919-0.1250370489580.3405186330430.1146782343150.598134408012-8.4909340452716.26606703849.77055234505
84.033431877720.193346509220.7124502944822.897574974580.7535592836783.27019379062-0.00383927387875-0.3669561276250.9150795456020.0892933860601-0.005098341353320.823239140138-0.470591062018-0.15771491326-0.01310193618220.465194463701-0.02012801633080.06738713969810.360452252229-0.1056981864630.57132837785-4.5476270442616.441653331519.3144521562
96.609168129621.56914981174-2.124775956085.3096890861-0.2142509596656.52283002013-0.00734679293073-0.361585510781-0.005755309577840.09772211106230.2117790348680.1930932166830.475794570092-0.24934008492-0.1303423545150.4565161668390.0290291015851-0.03787304897170.4926650091010.1311322786660.285425905641.75114846339-14.8057873423-3.17041004152
103.197021729161.42616268769-1.692191515432.24558676152-0.4239537274132.116450659170.0509043047597-0.003499578717180.00574290265824-0.0008858890697860.0540795407931-0.102892209654-0.260650499830.0357999361881-0.08959236138780.417023467118-0.0408568987268-0.05134830778210.3200397000720.04089829185230.26494085094510.30594729220.238186831381-12.4377588861
118.501701448775.050647800540.6905146173374.000493703652.575037983714.659311319870.005480065806350.6633315466790.608243897183-1.099600031690.06095148898730.63970814131-0.628680093617-0.409544073726-0.1115497129190.5272370720140.1126541303170.009833392813280.5267298275090.1325579163310.4270972725814.6278847056.13259322072-17.8613517095
128.131606996934.828953226852.492032050673.291640241330.9081602297042.419509128710.299098591809-0.838289540601-0.366966467386-0.0063729289545-0.240152764753-0.00840260449552-0.608714388576-0.202246357218-0.1187680952250.5118587178960.05204978446820.1122629068130.320926688587-0.03099420907430.4188878270919.176019622096.99974628532-4.48543512694
131.0004028898-0.290497480425-0.622900079942.618834884771.059393970441.91443082417-0.0349324148151-0.0114009128174-0.2352859199520.1758956751110.07329014478550.2668705968850.187649261405-0.1430144957870.06887129057380.357901353098-0.0483249580745-0.07858973960110.4417191971660.03815472435420.3782093272315.36946472944-18.3682755913-9.07241447238
142.098762377631.665285260830.3454148786993.206972551770.4745220220931.55299612688-0.2240929852460.101309651114-0.00750432950594-0.3317285085250.241330236529-0.0973457156817-0.2021064070090.0893081082094-0.0013019736470.405147481499-0.0284989820049-0.04545664096480.3700236511510.02968248674680.30109157298817.6100146301-7.79329148218-21.1806300992
152.55404992671.2213888454-0.3889616772742.80786477447-2.114231597243.09073971145-0.1065692711180.0127904561209-0.137882392213-0.02576046644210.0829459416997-0.4121709626030.05376344290150.03084030976060.03189942070290.416751047210.0359127596337-0.02333647032260.3957068388620.01495304070530.30638336358820.3624978676-21.7130754842-15.1407861711
163.721724664743.9399788487-0.258155418447.492738633110.03826850197991.24194113787-0.0873313176313-0.449661057091-0.0730863486522-0.08192652529650.0771330101109-0.478359971438-0.1667933779150.1349833924450.05471304392450.354909873362-0.02916466446320.01967353921250.4400825510710.01689226730020.28269097001125.4200778421-13.9279194958-19.1256266755
172.063176018260.56708207871-1.023300016723.97531106237-0.9606610316441.19475963636-0.1255574621370.432913498233-0.352734808562-0.53347751521-0.0329888900002-0.2168122131310.1665140483270.01440450879550.1615226504810.483192850935-0.0463288669650.03084478053270.418993790401-0.04707021089850.29420438607916.4995965421-25.8391076118-21.9217639843
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 44 through 62 )AA44 - 621 - 19
22chain 'A' and (resid 63 through 111 )AA63 - 11120 - 68
33chain 'A' and (resid 112 through 129 )AA112 - 12969 - 86
44chain 'A' and (resid 130 through 147 )AA130 - 14787 - 104
55chain 'A' and (resid 148 through 173 )AA148 - 173105 - 130
66chain 'A' and (resid 174 through 239 )AA174 - 239131 - 196
77chain 'A' and (resid 240 through 258 )AA240 - 258197 - 215
88chain 'A' and (resid 259 through 334 )AA259 - 334216 - 291
99chain 'B' and (resid 44 through 62 )BC44 - 621 - 19
1010chain 'B' and (resid 63 through 111 )BC63 - 11120 - 68
1111chain 'B' and (resid 112 through 129 )BC112 - 12969 - 86
1212chain 'B' and (resid 130 through 147 )BC130 - 14787 - 104
1313chain 'B' and (resid 148 through 173 )BC148 - 173105 - 130
1414chain 'B' and (resid 174 through 239 )BC174 - 239131 - 196
1515chain 'B' and (resid 240 through 264 )BC240 - 264197 - 221
1616chain 'B' and (resid 265 through 295 )BC265 - 295222 - 252
1717chain 'B' and (resid 296 through 334 )BC296 - 334253 - 291

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