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- PDB-9mua: 4OT-SnoaL from P. atlanticus - Apo form -

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Basic information

Entry
Database: PDB / ID: 9mua
Title4OT-SnoaL from P. atlanticus - Apo form
ComponentsTautomerase
KeywordsUNKNOWN FUNCTION / Tautomerase SnoaL-like
Function / homology4-oxalocrotonate tautomerase / Tautomerase enzyme / SnoaL-like domain / SnoaL-like domain / Tautomerase/MIF superfamily / NTF2-like domain superfamily / isomerase activity / Tautomerase
Function and homology information
Biological speciesPseudooceanicola atlanticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsMelkonian, T.R. / Vuksanovic, N. / Allen, K.N. / Whitman, C.P.
Funding support United States, 1items
OrganizationGrant numberCountry
Robert A. Welch FoundationF-2125 United States
Citation
Journal: Biochemistry / Year: 2025
Title: Beyond the beta-alpha-beta Fold: Characterization of a SnoaL Domain in the Tautomerase Superfamily.
Authors: Melkonian, T.R. / Vuksanovic, N. / Person, M.D. / Chen, T.Y. / Chang, W.C. / Allen, K.N. / Whitman, C.P.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2May 14, 2025Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tautomerase
B: Tautomerase
C: Tautomerase
D: Tautomerase
E: Tautomerase
F: Tautomerase


Theoretical massNumber of molelcules
Total (without water)126,2276
Polymers126,2276
Non-polymers00
Water9,944552
1
B: Tautomerase
C: Tautomerase
D: Tautomerase
E: Tautomerase

A: Tautomerase

F: Tautomerase


Theoretical massNumber of molelcules
Total (without water)126,2276
Polymers126,2276
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
crystal symmetry operation4_455x-1/2,-y+1/2,-z1
Buried area24360 Å2
ΔGint-151 kcal/mol
Surface area45260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.779, 104.256, 193.745
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+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Tautomerase


Mass: 21037.797 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudooceanicola atlanticus (bacteria) / Gene: ATO9_16250 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A0EFB9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / 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: 3.27 Å3/Da / Density % sol: 62.4 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop
Details: 9 mg/mL protein, 0.2 M sodium thiocyanate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.97→50.68 Å / Num. obs: 117762 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 38.68 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.178 / Rpim(I) all: 0.05 / Net I/σ(I): 9.7
Reflection shellResolution: 1.97→2.02 Å / Redundancy: 12.1 % / Rmerge(I) obs: 5.184 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 5853 / CC1/2: 0.433 / Rpim(I) all: 1.544

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→50.68 Å / SU ML: 0.2763 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5839
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2407 2000 1.72 %
Rwork0.1988 114549 -
obs0.1995 116549 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.84 Å2
Refinement stepCycle: LAST / Resolution: 1.97→50.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8856 0 0 552 9408
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01159060
X-RAY DIFFRACTIONf_angle_d1.106112318
X-RAY DIFFRACTIONf_chiral_restr0.06041368
X-RAY DIFFRACTIONf_plane_restr0.01331620
X-RAY DIFFRACTIONf_dihedral_angle_d14.81323360
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.020.36021260.35157260X-RAY DIFFRACTION88.68
2.02-2.070.35751400.33418006X-RAY DIFFRACTION98.12
2.07-2.130.34531430.3018178X-RAY DIFFRACTION99.72
2.13-2.20.30311440.27548167X-RAY DIFFRACTION99.82
2.2-2.280.29241420.25498200X-RAY DIFFRACTION99.95
2.28-2.370.25321430.23118170X-RAY DIFFRACTION99.92
2.37-2.480.29771430.22428214X-RAY DIFFRACTION99.86
2.48-2.610.27121440.21848206X-RAY DIFFRACTION99.78
2.61-2.780.28081430.21988210X-RAY DIFFRACTION99.93
2.78-2.990.28281440.22088279X-RAY DIFFRACTION99.99
2.99-3.290.25521450.2148291X-RAY DIFFRACTION99.93
3.29-3.770.22591450.18758295X-RAY DIFFRACTION99.89
3.77-4.740.20221460.14338404X-RAY DIFFRACTION99.95
4.74-50.680.18791520.16838669X-RAY DIFFRACTION99.71
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)
18.637818597520.3395475036290.7341060545285.00570625427-1.187157013125.07063211916-0.0710552470722-0.739149955615-0.6121437029670.363013322869-0.269336214928-0.7877745343280.2119529365530.3910187857710.3375617602440.3245922918820.0178768493494-0.02170587674750.3436000026090.101669657050.3447893076477.2879782141716.146431867515.6156372227
23.770193454985.25534924157-1.106420356588.70047635098-2.207994933314.95314496193-0.154556359755-0.333921814427-0.354405182856-0.06343354195120.0771052739178-0.1608093482730.1490980205160.02801251660780.1481543836630.202501362760.0543730111444-0.04996642984320.3453212873410.03106598249390.4241086632484.9136461063220.865631505811.1331412383
34.51111363692-2.314543049422.533681982744.338525215650.4159663412122.85068922440.366062748767-0.6503250644880.454492655881-0.130005769851-1.34523857-0.484568591837-0.8736634297210.7090233972661.056325275290.756786732798-0.048204312412-0.1522666378060.7503227825820.100622677910.62742702494313.673044806428.255856963920.8366748797
46.381425960630.486869237679-0.6500488648887.472715490541.925512831522.94493031982-0.08042861640280.0900382161590.1308977753270.0126613596876-0.209631424265-0.6412321892050.2360354627940.8323565396760.2827490729070.338573716553-0.0714571136312-0.05245595246510.7489654803260.2388385851220.43255226238319.624086607811.70459401540.7180745468
54.475564793520.564276382228-0.3979470323886.38441881558-1.571521456073.22045648658-0.0220313651903-0.6753572295230.3339824502320.9096304796310.132724037707-0.170525645994-0.560029936565-0.113311738396-0.06585028179810.412331573708-0.019936901191-0.0780246740140.6832283117910.1054308493620.4202253222159.1915768874717.044269068848.7717662966
62.7759755482-0.9509053329140.3970060486572.77152611397-0.7289143400662.08246911432-0.124754569274-0.09649319717770.06528945237820.141781382758-0.00399375492636-0.228128616201-0.0792049610385-0.06262052033290.1384239269520.350870049513-0.0328375549705-0.03063844067110.6685039614630.1719308158860.390208333299.965057210256.1262505099843.7397127221
77.53024391908-2.65120483414.877043322744.309665986141.476805317936.20691687702-0.332710548284-0.537351493840.01591118749680.534901920899-0.1110799893850.120116964180.1596807473160.4079468996240.482200994020.507733286024-0.0444178079652-0.0002807972903070.7391087273270.2553106327840.4495667483624.48423934563-4.0598341973655.0057206495
86.15465991698-1.28622842046-1.421951217591.423196910081.654052681764.14047073154-0.10362571145-0.2923068575740.1893438088990.195425741778-0.02771035864210.2027637613410.118134773606-0.07051974600250.1145238069230.245970414670.018056039434-0.002377611295890.2402220828970.006556718454170.22978897198933.889407355332.65079384627.66917719011
96.599497395831.64117881047-0.7851993534097.36281407101-2.094136831561.6334969192-0.118871729857-0.0572509197935-0.01471801314060.212226151004-0.09686995048070.556794196436-0.295838153393-0.3392652833020.2142342876260.3463738814-0.03087185579460.02712157587790.695027436249-0.2013882675290.34952909251121.295637548441.846427847533.1787823311
102.67347032233-0.008001493364510.6895050755364.491984984361.313523398841.78659545036-0.0777071006274-0.5426854389190.01135440736470.521235050821-0.09090973496670.302048519320.169423017224-0.3086838392120.1356675899620.313735447339-0.0007221893604360.02064112925910.726712218104-0.1579683018780.36241799876629.735521735743.636180655339.7782173317
112.65790388843-1.23285064646-0.7447463799462.664338200581.997619070393.82372358884-0.068875370632-0.2472243976010.2290902960240.1206266461720.01350870533770.130733560092-0.03906357274160.09619402497590.0479259978550.360731782647-0.06266430695980.0316406007370.679704500353-0.1619930224010.34854312830533.082675376648.816834449436.8511271582
128.52913293406-0.2675493264893.837122507424.47349777355-0.4996315878763.717714779190.156386358486-0.136387301116-0.5340199374980.004491593030720.01923004482890.8682161571150.236339996807-0.195688132529-0.1941770028760.23593038999-0.0114200531640.06330979145780.2116774266630.02796567969060.3762342765634.911763495813.1295342372-1.74518395833
134.04588168425-0.09734572854711.883728769994.90091263205-1.126674906761.87135129906-0.1980117474790.470645470214-0.319801157253-0.3022226193590.2289984689130.309676761607-0.008266675372990.240667757568-0.01819882212480.285775075589-0.01715650929230.07025908586930.366383291081-0.03319838572930.38528676352834.718775080217.4181373535-7.2716497841
146.104050710240.009160615502140.01428845298442.14783015942-1.289403428098.083892074850.009427456527850.191632353883-0.0419323423795-0.05512922982390.2679837173140.6504712496270.13577520262-0.500991617147-0.1836990831140.3445743361630.00439430408929-0.08064230727950.3206610480740.03056733722480.84207179860423.5494885158-11.847124625-6.77063494669
152.388249528760.0832698476163-0.293495146442.09250209972-0.220202490112.74614427708-0.04753345707950.256532470918-0.346534123121-0.1465932029120.1322502961620.1044717856410.315001049015-0.183966841261-0.07795518969430.336029021346-0.0225862509807-0.04216278537120.2712852029170.0274255799610.69284095662932.1588008285-18.1792123135-7.24299907419
162.645782787840.753114796294-0.3725253210333.206452404040.4007473957580.7948805440780.0852356531877-0.093815244123-0.1464745801750.03177853055750.05957336068220.281432635118-0.00928946191180.027184931612-0.1665763109540.259287875984-0.0015192780072-0.02701528014590.2532012097210.04409956060710.62549696640934.4577294091-15.1380691789-2.16412193093
170.11996067751-0.150997169802-0.707487467591.96422788718-1.078259672056.6861009609-0.131469062084-0.268738193277-1.01588977353-0.4993526456620.352582260024-0.3753023879850.8680638130450.0570732434611-0.2009873212960.433059835991-0.0255782477044-0.05551327899220.3105262782170.1149578856380.91905976315838.6243840782-30.36217314423.55796031337
186.416852849520.05408288648821.145043326654.899987829431.175649493322.8742901924-0.1028968280210.0777602048219-0.2876043042110.001230657898880.144392152447-0.189365284606-0.01372666104140.110112779138-0.0428299261270.2019185237130.007626479781150.02173965561170.1947495306080.04848108682080.18977950384647.17950597316.2112125554-3.20826472199
191.28506653942-0.3180412527630.1661062526323.433814204590.7145703370451.24723626566-0.0532642831069-0.257229559633-0.3780551717570.1896309243640.159669491494-0.3582606614880.02216700713940.0497495024073-0.1012805842710.2979882541120.014071025481-0.03970779559010.3016193028380.07791471958020.61689474857754.8833473312-10.95717077375.78486045958
201.70279740286-1.12436862335-0.590034992325.288851565630.7981050439091.531638759230.001213449122390.0686551879163-0.2572381565250.1261541670830.01417914196090.03453595651710.1785895655330.05072634213880.002948148869050.3210360697450.000669071913964-0.04484485064710.2692035721820.05772398806660.65411047308249.1373518664-17.5164434622-0.209302492757
216.747421310061.61518088553-2.689274255281.91607508772-0.01870551915926.95661913845-0.0306215460122-0.4770415324730.2162455512440.05510019432250.0166308167246-0.13398246483-0.1631124514350.5860385847520.01431230411330.2535211512180.0266937829538-0.04357505297470.256134663149-0.0494188661240.32088818105946.424677266233.94833014916.86704900943
220.285266305935-0.0687974481114-0.9611973391991.627694292880.4904552385013.64065759263-0.0657745779525-0.01981307833110.355160855214-0.07354419594650.169342939489-0.0816565457922-0.2013103417040.214907326318-0.1144185086530.359247154972-0.0904189619994-0.02453809065240.727991971528-0.1810518346120.55862229727552.449546993652.8975239827.979501601
234.006236691970.3873269697481.281186678921.49142244510.110336306563.25348872248-0.0916683434017-0.09176453534950.1007276462520.12840545482-0.0381227909955-0.07559226522520.0493117963844-0.1289960700440.136226203960.332271584591-0.03614628003910.005923624919560.563973766894-0.1481953769490.35613028750148.159913193549.339722411235.5172430318
243.918407991262.734016187043.531458135823.23837725941.14522237034.79683541974-0.0193972259434-0.2270832103270.1408762735920.1854211480540.2970206206710.302613127878-0.1000752909640.891643221111-0.3453017335580.384493875812-0.06635394068830.03675547655830.743093287721-0.2013546633770.41517082254943.474488893251.881891106550.0329868522
258.576642254192.108363291291.107122856884.37763329827-0.4812026211355.26527939734-0.0340187148539-1.11222147818-0.2779593650790.4581646924920.05635505891940.1515461131640.2944931011-0.76831064931-0.01264850461920.3126788286480.01432637742330.02957737943850.4436709351060.09399242397410.28878155515975.614464439518.521687987817.0566419305
261.082699956840.190052269332-0.2657898721041.11256427413-2.379557285865.00628569734-0.0377617288627-0.193105143366-0.3533934414490.01152980726680.152685300096-0.09803854542780.404273575701-0.46475255917-0.1304128341940.3587545825220.01057935628260.008825928598050.4380159798780.07465574062660.43377571026972.91109115613.102312053217.4469986198
277.43842309386-0.504361817199-5.459246687196.82508350124.399628983027.51632720308-0.3026026551170.0641771276098-0.1062554398110.1587123618620.05387671453940.9092951761640.507824397603-0.3419504648340.2046880741330.349942745848-0.18210858131-0.005271006761170.8928326652630.1321285813740.54427929296461.1725741537-2.4958655064836.394487479
282.59215675039-0.142660383535-0.62366250421.96993727824-0.2477976038973.18077384075-0.026262964265-0.115024733782-0.213336318950.09042552468410.04988409196250.1004851086680.117038089215-0.222668332448-0.0444352758680.317155266336-0.0385253646356-0.03136434190890.6646436829510.1966402974970.40134712743674.29877837521.2947343426443.0382609833
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 29 )AA1 - 291 - 29
22chain 'A' and (resid 30 through 54 )AA30 - 5430 - 54
33chain 'A' and (resid 55 through 65 )AA55 - 6555 - 65
44chain 'A' and (resid 66 through 88 )AA66 - 8866 - 88
55chain 'A' and (resid 89 through 105 )AA89 - 10589 - 105
66chain 'A' and (resid 106 through 177 )AA106 - 177106 - 177
77chain 'A' and (resid 178 through 186 )AA178 - 186178 - 186
88chain 'B' and (resid 1 through 65 )BB1 - 651 - 65
99chain 'B' and (resid 66 through 88 )BB66 - 8866 - 88
1010chain 'B' and (resid 89 through 131 )BB89 - 13189 - 131
1111chain 'B' and (resid 132 through 186 )BB132 - 186132 - 186
1212chain 'C' and (resid 1 through 29 )CC1 - 291 - 29
1313chain 'C' and (resid 30 through 65 )CC30 - 6530 - 65
1414chain 'C' and (resid 66 through 88 )CC66 - 8866 - 88
1515chain 'C' and (resid 89 through 132 )CC89 - 13289 - 132
1616chain 'C' and (resid 133 through 177 )CC133 - 177133 - 177
1717chain 'C' and (resid 178 through 186 )CC178 - 186178 - 186
1818chain 'D' and (resid 1 through 54 )DD1 - 541 - 54
1919chain 'D' and (resid 55 through 132 )DD55 - 13255 - 132
2020chain 'D' and (resid 133 through 186 )DD133 - 186133 - 186
2121chain 'E' and (resid 1 through 54 )EE1 - 541 - 54
2222chain 'E' and (resid 55 through 136 )EE55 - 13655 - 136
2323chain 'E' and (resid 137 through 177 )EE137 - 177137 - 177
2424chain 'E' and (resid 178 through 186 )EE178 - 186178 - 186
2525chain 'F' and (resid 1 through 29 )FF1 - 291 - 29
2626chain 'F' and (resid 30 through 78 )FF30 - 7830 - 78
2727chain 'F' and (resid 79 through 88 )FF79 - 8879 - 88
2828chain 'F' and (resid 89 through 186 )FF89 - 18689 - 186

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