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- PDB-7mgq: AICAR transformylase/IMP cyclohydrolase (ATIC) is essential for d... -

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Basic information

Entry
Database: PDB / ID: 7mgq
TitleAICAR transformylase/IMP cyclohydrolase (ATIC) is essential for de novo purine biosynthesis and infection by Cryptococcus neoformans
Components5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
KeywordsSTRUCTURAL PROTEIN / Isomerase / ligand / complex
Function / homology
Function and homology information


phosphoribosylaminoimidazolecarboxamide formyltransferase activity / IMP cyclohydrolase activity / 'de novo' IMP biosynthetic process
Similarity search - Function
AICAR transformylase, insert domain superfamily / AICAR transformylase, duplicated domain superfamily / AICARFT/IMPCHase bienzyme / Bifunctional purine biosynthesis protein PurH-like / AICARFT/IMPCHase bienzyme / MGS-like domain profile. / Methylglyoxal synthase-like domain / Methylglyoxal synthase-like domain superfamily / MGS-like domain / MGS-like domain / Cytidine deaminase-like
Similarity search - Domain/homology
Phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase
Similarity search - Component
Biological speciesCryptococcus neoformans (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsWizrah, M.S. / Chua, S.M.H. / Luo, Z. / Manik, M.K. / Pan, M. / Whyte, J.M. / Robertson, A.B. / Kappler, U. / Kobe, B. / Fraser, J.A.
Funding support Australia, 1items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia) Australia
CitationJournal: J.Biol.Chem. / Year: 2022
Title: AICAR transformylase/IMP cyclohydrolase (ATIC) is essential for de novo purine biosynthesis and infection by Cryptococcus neoformans.
Authors: Wizrah, M.S.I. / Chua, S.M.H. / Luo, Z. / Manik, M.K. / Pan, M. / Whyte, J.M.L. / Robertson, A.A.B. / Kappler, U. / Kobe, B. / Fraser, J.A.
History
DepositionApr 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 2, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
B: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
C: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
D: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)262,0328
Polymers261,9354
Non-polymers974
Water1,33374
1
A: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
B: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0164
Polymers130,9672
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
C: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
D: 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,0164
Polymers130,9672
Non-polymers492
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.841, 115.867, 111.823
Angle α, β, γ (deg.)90.000, 96.183, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUPROPRO(chain 'A' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))AA4 - 4884 - 488
12ALAALAGLUGLU(chain 'A' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))AA496 - 512496 - 512
13ALAALAHISHIS(chain 'A' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))AA519 - 605519 - 605
21GLUGLUPROPRO(chain 'B' and (resid 4 through 512 or resid 519 through 605))BB4 - 4884 - 488
22ALAALAGLUGLU(chain 'B' and (resid 4 through 512 or resid 519 through 605))BB496 - 512496 - 512
23ALAALAHISHIS(chain 'B' and (resid 4 through 512 or resid 519 through 605))BB519 - 605519 - 605
31GLUGLUPROPRO(chain 'C' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))CC4 - 4884 - 488
32ALAALAGLUGLU(chain 'C' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))CC496 - 512496 - 512
33ALAALAHISHIS(chain 'C' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))CC519 - 605519 - 605
41GLUGLUPROPRO(chain 'D' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))DD4 - 4884 - 488
42ALAALAGLUGLU(chain 'D' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))DD496 - 512496 - 512
43ALAALAHISHIS(chain 'D' and (resid 4 through 488 or resid 496 through 512 or resid 519 through 605))DD519 - 605519 - 605

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Components

#1: Protein
5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase / AICAR transformylase / IMP synthase / Inosinicase / Phosphoribosylaminoimidazolecarboxamide formyltransferase


Mass: 65483.727 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans (fungus) / Gene: C356_00722 / Production host: Escherichia Coli (E. coli) / Strain (production host): BL21-Gold(DE3)pLysS AG
References: UniProt: A0A225ZZG7, phosphoribosylaminoimidazolecarboxamide formyltransferase, IMP cyclohydrolase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 45.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.2 M MgCl2, 20% w/v PEG 6000 and 0.2 M Tris base / PH range: 6.5-8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.954 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.67→48.92 Å / Num. obs: 65094 / % possible obs: 98.75 % / Redundancy: 2 % / Biso Wilson estimate: 60.87 Å2 / CC1/2: 0.999 / Net I/σ(I): 71.97
Reflection shellResolution: 2.674→2.77 Å / Num. unique obs: 6258 / CC1/2: 0.907

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PKX

1pkx


Resolution: 2.67→48.92 Å / SU ML: 0.3693 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.0365 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2346 1999 3.07 %
Rwork0.199 63086 -
obs0.2001 65085 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 69.4 Å2
Refinement stepCycle: LAST / Resolution: 2.67→48.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18193 0 4 74 18271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002918549
X-RAY DIFFRACTIONf_angle_d0.638325124
X-RAY DIFFRACTIONf_chiral_restr0.04422852
X-RAY DIFFRACTIONf_plane_restr0.0043267
X-RAY DIFFRACTIONf_dihedral_angle_d14.15311293
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.740.34911330.31754201X-RAY DIFFRACTION92.55
2.74-2.810.3161430.29244507X-RAY DIFFRACTION98.73
2.81-2.90.32841430.27824499X-RAY DIFFRACTION98.89
2.9-2.990.2981410.27134469X-RAY DIFFRACTION98.86
2.99-3.10.28061440.264517X-RAY DIFFRACTION98.98
3.1-3.220.28981430.26554502X-RAY DIFFRACTION99.06
3.22-3.370.29081420.24194507X-RAY DIFFRACTION99.08
3.37-3.550.26171430.21474512X-RAY DIFFRACTION99.15
3.55-3.770.25541430.19974500X-RAY DIFFRACTION99.23
3.77-4.060.21231430.18714547X-RAY DIFFRACTION99.3
4.06-4.470.18951440.16674562X-RAY DIFFRACTION99.41
4.47-5.110.19991450.15634547X-RAY DIFFRACTION99.39
5.11-6.440.241450.18734578X-RAY DIFFRACTION99.62
6.44-48.920.18571470.16134638X-RAY DIFFRACTION99.44
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)
12.68488234776-0.562404688361.635694851043.0995825294-1.109349056761.99543054762-0.280357250083-0.03424747313311.16432015460.303313337471-0.2511363087070.00241138467709-0.6993821376660.2214660120810.4361406919220.387394689-0.0442445021286-0.1010959611630.4199415860380.01612282316510.837486594097-23.252353192229.215570008-56.6653927566
25.491968313060.04195467153141.06867546372.89211933498-0.3242950007972.013477046020.344257071102-1.25142122166-0.8239592298610.731072333136-0.203950209104-0.4335531931970.270255760916-0.0654778667666-0.140701091620.608203518361-0.171483313396-0.1096879118590.6182583008590.1954245199390.6046458653922.139486297693.99874307263-33.1306191279
36.04309831793-0.656891033226-0.1564685086912.697279482850.3917371584072.32095517528-0.07993076956040.329434093317-0.9089392650060.0326756400040.03713911095750.09441672011450.5556816634660.2724979128390.04221245178030.448184078072-0.0229837130661-0.01191724417680.4671525471530.03657988094820.57108651652113.869203033312.6039883669-51.284664595
43.096691576140.01591205414340.627863599612.30308710399-0.6096220870036.153090250190.254432053584-1.1721389305-0.4199382329040.948817986708-0.310089923378-0.446482082612-0.1981076914630.526164060984-0.01339630093220.646314613912-0.188115470478-0.147484429630.9034001397140.2076969928130.69216971774825.183156419911.5835212128-26.8979722054
53.56445156043-0.130594834789-0.316230192774.6986680697-1.225104592157.86536823783-0.06782261670530.566523909279-0.0462367827434-0.245400656258-0.434012475567-0.451294744342-0.3405146746660.6975448936190.4215682184620.371454279869-0.0391762322054-0.001521470540350.5750301006570.05897941423690.61728285765929.998457242115.7319912995-47.0363882029
66.07631891625-2.83222199521.177123667656.673307166540.08621873873194.877608156170.2950743861360.532270008182-0.449103149933-0.423512955935-0.0677394922192-0.02922433450.486848514570.178597318957-0.1581210672220.3151388466-0.0226829420672-0.07941084606320.372590833394-0.03126418193870.504501084325-34.06106698475.60663775154-66.959926401
74.585700608991.802870544361.214968983071.349777663550.6353767142271.35318455767-0.0956795322190.5454755403270.0949364930966-0.1537567919290.0121257291951-0.230951493712-0.1234924283820.3228974662660.0846302334010.3103247884820.03867066276890.00783151954650.4073241176080.08285555499660.537664752476-10.909760768519.9510857327-58.0147886544
83.298396517451.185679217412.185817003682.802344420461.092705351052.77676247583-0.0823425365033-0.2019917113511.140177490280.122198315686-0.1014883723980.332767702006-0.4125393552140.4175980838530.1488648320770.461487668034-0.1285762932970.1362191933870.613764740096-0.07922263372550.80215957691111.8494640438.0172469526-36.9054574728
97.475933453890.0672754581512-1.114982268351.231238948410.2639143624271.77424812950.129751114967-1.196213453080.1969289031750.54480684966-0.2593457323740.0296958499492-0.01146870125760.1601064273540.1175149611990.758723414113-0.263335051312-0.01223050199850.836546552369-0.06623206536010.51247294962323.589431193132.0543412907-24.4364706417
103.919139147060.3559356088051.276860389712.852999847930.3251920965284.21391306286-0.191123889139-0.2849149034860.7886895550960.0946083486748-0.08947264339250.466429621446-0.615594074437-0.5063026951710.2860488752970.3621296187340.0780043519965-0.08715497927210.392823377974-0.07360592590560.644935339494-24.316604915890.242750611-32.4993355648
113.46910419811-0.9980977743891.18213172032.62694109244-1.697651923624.32586374218-0.0974481826428-0.4282374768960.234763079910.495532737414-0.05420222911390.15967370398-0.439967603402-0.09278619681260.1312161540970.303685651414-0.015347568466-0.006734146798210.381717580727-0.08206672243850.402497402758-11.990865798480.9171317726-19.9224651989
126.27261897829-2.00526716430.7773836287023.384732738580.1569316387891.77530772563-0.0678024949463-0.748510445857-0.3595109550230.7131905146560.269406356492-0.1713639083780.337048598823-0.205447901339-0.2277261864340.623105937931-0.01538792854460.02084678417620.45985794070.05165742151120.31968822724815.239726295557.54016308920.498319496575
133.6872450483-0.7506884993271.669030703362.56742341737-0.5497549902531.857197056240.246365837747-0.00696690030103-0.468232823010.134508384518-0.0151228878322-0.1099378850270.7718340097020.134227219381-0.2223299333680.7079094043690.0731242724088-0.03827677676760.420242636972-0.04573923127370.30955166521819.00464861958.8709818754-6.27715267125
143.181768542190.2700125875060.6946524141134.09740703551-1.354529998349.562040409740.146999708388-0.947738799525-0.09972424430561.06025449475-0.133915150342-0.321033010101-0.3226869802630.176677488047-0.01933622627840.6942603906180.0633572742237-0.1215834245330.713621775133-0.02909632291550.49956296987536.855523443362.210219018811.4995294527
154.63689822212-2.28726329277-4.703927970496.205636342221.799438796694.90444779720.1567561657960.5702819957660.133334803729-0.256825568137-0.167166299348-0.815369490671-0.3182781813690.5078054498830.06981511897740.5721851000630.0613981395263-0.02953615350040.668193684835-0.02221262321160.57640447646639.746737551465.1273682901-13.9045395713
164.90363092864-1.327962532431.133157304065.566251226680.7707454871044.057793037290.4466373251670.189567192991-1.01722936289-0.325810522673-0.2562917798030.249990506070.57074628948-0.308366222122-0.1522689507410.407724714823-0.0504406664175-0.1175936882560.367092954947-0.02761564902440.552071907325-25.634766569662.5590848896-33.0752015369
175.521156430580.9448045004270.4567993632692.147529196360.4998970662222.040935296320.10381106863-0.12629376267-0.648187100427-0.134934636703-0.216289159946-0.04636885368290.3107389461440.1211707271750.09044642655780.3265039485570.0585659590401-0.03890146827740.3197713075370.04649816465670.368312368932-8.0655377655270.1514107691-27.0500063819
184.917189293991.725345550262.470682065674.655589078531.120038781795.16030727334-0.4192100288570.4759271008340.7757207660070.2075747441330.131563368069-0.648536758426-0.6986362482980.7928620260490.2623476171050.477414071788-0.0256199862509-0.06600836405350.4878271925410.1048777827350.56653115755223.729766812791.3125441544-11.8627407298
193.873673779171.53698130982.506744404612.956353390170.9135251503693.36423724107-0.270553624422-0.4781305495450.5221059747970.789233163752-0.0235381125945-0.236784862153-0.2130212433990.09248557098730.2871642777880.6908297178290.10749343601-0.09899414177110.531788214225-0.04686249410710.46283062453723.276729824684.44572587925.11497969536
203.532379878810.3908261701270.7309535161132.02777768515-0.1822639961783.06274352171-0.223226011612-0.7002203952010.1030562953560.642129268819-0.164782453233-0.322452897559-0.2783191493670.294178777890.3337551644630.8734658937790.0571094849033-0.1981101662580.693942645082-0.07733711404230.57000578081932.040427630481.442334840712.1286822931
213.24455108660.02603015217461.629747721774.581988695911.044962788313.1228057216-0.4458616888450.1527638774051.19122985924-0.129309971147-0.03201536229710.321404564208-0.615071491316-0.1611628687620.4576847590220.388999385147-0.026693337319-0.1810105133390.4463312202270.1019940449950.941660294113-35.900498677533.2356175872-66.4350224828
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'C' and (resid 99 through 196 )
2X-RAY DIFFRACTION2chain 'C' and (resid 197 through 386 )
3X-RAY DIFFRACTION3chain 'C' and (resid 387 through 422 )
4X-RAY DIFFRACTION4chain 'C' and (resid 423 through 557 )
5X-RAY DIFFRACTION5chain 'C' and (resid 558 through 605 )
6X-RAY DIFFRACTION6chain 'D' and (resid 4 through 98 )
7X-RAY DIFFRACTION7chain 'D' and (resid 99 through 269 )
8X-RAY DIFFRACTION8chain 'D' and (resid 270 through 480 )
9X-RAY DIFFRACTION9chain 'D' and (resid 481 through 605 )
10X-RAY DIFFRACTION10chain 'A' and (resid 4 through 98 )
11X-RAY DIFFRACTION11chain 'A' and (resid 99 through 217 )
12X-RAY DIFFRACTION12chain 'A' and (resid 218 through 337 )
13X-RAY DIFFRACTION13chain 'A' and (resid 338 through 461 )
14X-RAY DIFFRACTION14chain 'A' and (resid 462 through 557 )
15X-RAY DIFFRACTION15chain 'A' and (resid 558 through 605 )
16X-RAY DIFFRACTION16chain 'B' and (resid 4 through 98 )
17X-RAY DIFFRACTION17chain 'B' and (resid 99 through 218 )
18X-RAY DIFFRACTION18chain 'B' and (resid 219 through 386 )
19X-RAY DIFFRACTION19chain 'B' and (resid 387 through 500 )
20X-RAY DIFFRACTION20chain 'B' and (resid 501 through 605 )
21X-RAY DIFFRACTION21chain 'C' and (resid 4 through 98 )

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