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- PDB-9vnu: Crystal structure of chimeric AIR synthetase constructed from E. ... -

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Basic information

Entry
Database: PDB / ID: 9vnu
TitleCrystal structure of chimeric AIR synthetase constructed from E. coli (residues 1-168) and Pyrococcus abyssi (residues 163-334)
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 / purine nucleotide biosynthetic process / '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 / Phosphoribosylformylglycinamidine cyclo-ligase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Pyrococcus abyssi GE5 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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


Theoretical massNumber of molelcules
Total (without water)37,1101
Polymers37,1101
Non-polymers00
Water2,018112
1
A: Phosphoribosylformylglycinamidine cyclo-ligase

A: Phosphoribosylformylglycinamidine cyclo-ligase


Theoretical massNumber of molelcules
Total (without water)74,2202
Polymers74,2202
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545x,-y-1,-z1
Buried area3250 Å2
ΔGint-32 kcal/mol
Surface area25390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.911, 45.205, 75.170
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number17
Space group name H-MP2221
Space group name HallP2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21A-468-

HOH

31A-495-

HOH

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Components

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


Mass: 37109.750 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Pyrococcus abyssi GE5 (archaea)
Gene: purM, purG, b2499, JW2484, purM, PYRAB16520, PAB1083 / Production host: Escherichia coli (E. coli)
References: UniProt: P08178, UniProt: Q9UY56, phosphoribosylformylglycinamidine cyclo-ligase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
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: 2.26 Å3/Da / Density % sol: 45.68 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: pentaerythritol ethoxylate (3/4 EO/OH), magnesium chloride

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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: Nov 30, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. obs: 13687 / % possible obs: 99.8 % / Redundancy: 6.6 % / Biso Wilson estimate: 36.76 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Net I/σ(I): 15.71
Reflection shellResolution: 2.4→2.59 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.614 / Mean I/σ(I) obs: 3.44 / Num. unique obs: 2664 / CC1/2: 0.994 / % possible all: 99.4

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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: 2.4→28.9 Å / SU ML: 0.1924 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 21.3753
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2227 691 5.05 %
Rwork0.1909 12992 -
obs0.1925 13683 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.2 Å2
Refinement stepCycle: LAST / Resolution: 2.4→28.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 0 112 2583
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00382514
X-RAY DIFFRACTIONf_angle_d0.59823398
X-RAY DIFFRACTIONf_chiral_restr0.0442388
X-RAY DIFFRACTIONf_plane_restr0.0057436
X-RAY DIFFRACTIONf_dihedral_angle_d4.9823349
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.590.29351300.23372534X-RAY DIFFRACTION99.48
2.59-2.850.25661290.21942554X-RAY DIFFRACTION99.89
2.85-3.260.23531400.21192577X-RAY DIFFRACTION99.96
3.26-4.110.23441550.17452581X-RAY DIFFRACTION100
4.11-28.90.18241370.17482746X-RAY DIFFRACTION99.9
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)
13.457504903511.046879430240.3386292571463.547503883690.6844191888722.06961814850.1347579963380.0470035647817-0.3018940632310.0911289037633-0.0484158890544-0.2794195973010.1300909374810.14602954055-0.03547322688810.2606997064070.0674852194930.007185379328060.2962515988590.06203651075140.255752869195-19.0042974375-31.4174817093-4.40159646222
23.962760838610.1338117829830.05510432672171.26124901398-0.3209722729081.23508026123-0.1113341765220.1035514561050.152438384995-0.3417862351560.03019355102740.0131064122686-0.0447678478764-0.1016386053070.01442263634350.3106767959920.0462436654228-0.03336121980860.32134207230.01996726339120.266738525719-32.5053552036-22.4944400536-13.6722817987
34.049536893541.75105579526-0.08518814938812.035884183180.2522804689521.09235662786-0.09181575849280.112081610418-0.323189843658-0.1733077856040.053100471501-0.0291675921520.180223683396-0.0182344636186-0.008821841696250.2744227469020.0335686594452-0.02818436683540.259299742914-0.0003546724469270.252682673919-28.5803543526-30.2387286449-7.89002689268
43.639068619010.514596902908-0.386352651091.03542352175-0.4735148794460.7925477303220.0345337411251-0.281792399583-0.1885051991080.0407959766676-0.0981809831456-0.06303433948520.101935690494-0.04519500927110.003381015684750.3383477669280.02215495322710.01261616033210.3238032806-0.03357521929310.297715423258-28.573952911-25.128975894-3.15948850964
51.92428973770.4149367267740.4130683081931.62596478997-0.1411017775181.298753247090.217333698805-0.07877404791410.3746789955910.106876517288-0.160834760508-0.262109297219-0.1039589327340.2078965298530.07106003211770.354672731532-0.02403402160610.04352197659760.3596922363830.01079601588890.427610377599-18.1038764675-8.60367189344-20.3971291888
64.36546987756-0.3357902860041.448698967931.26426951574-0.20629871211.33197670120.0684566073360.246398215545-0.184572384695-0.0919439679109-0.0425649047789-0.05135339679690.158788161716-0.0194740086755-0.03076307825760.340764250850.02201207551220.04715638307560.3141757878070.01343263863760.2283077563-31.5545588178-18.011479203-23.5310319516
75.341177796691.931357361681.722654779282.726236964380.6040172566141.123195519070.136562167303-0.1433972611520.7248089710420.204340118081-0.10732017592-0.256569819605-0.2771661898040.06020163616380.08939705400860.317537307507-0.0267382360610.01015329482910.260562126213-0.04323362205860.446763923741-21.5705371153-2.04800187392-19.2652160097
85.855397788520.2978347833681.348913123611.51650397793-0.5995203909961.549234601280.03810240348810.4539838765520.493565305568-0.2278867106830.04256275245520.0587842794436-0.0860322823912-0.0611474160945-0.07575869485830.320334478913-0.01957889863440.04664925780030.2968722825150.04388942098510.300211100991-31.3613343305-7.7146483632-27.3414254307
92.786244961340.397965818410.31856623752.75844707719-0.3386263177671.77206062151-0.1315237822410.8424395249560.112287621569-0.8910430576750.139161912973-0.3726818481770.09085341591220.7240044502640.06075923239750.4268625832170.03873807121550.1444497246160.4461363495470.02629534286310.414018587606-13.0325934261-12.504129224-29.5530573451
104.063181064461.796044197262.294056865282.398258077130.7029294224923.695199146920.0354486626408-0.01014070425361.022490417930.08003112563580.08072684604370.268699493412-0.890814522879-0.1939947237420.1716711314950.47808242259-0.07518405013060.0715626430430.3723570647040.08482762522470.726417928978-23.77204523733.88650548816-26.9383013796
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 16 through 69 )16 - 691 - 48
22chain 'A' and (resid 70 through 100 )70 - 10049 - 79
33chain 'A' and (resid 101 through 135 )101 - 13580 - 114
44chain 'A' and (resid 136 through 170 )136 - 170115 - 149
55chain 'A' and (resid 171 through 195 )171 - 195150 - 174
66chain 'A' and (resid 196 through 247 )196 - 247175 - 226
77chain 'A' and (resid 248 through 266 )248 - 266227 - 245
88chain 'A' and (resid 267 through 303 )267 - 303246 - 282
99chain 'A' and (resid 304 through 327 )304 - 327283 - 306
1010chain 'A' and (resid 328 through 342 )328 - 342307 - 321

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