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- PDB-7jtz: Yeast Glo3 GAP domain -

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Basic information

Entry
Database: PDB / ID: 7jtz
TitleYeast Glo3 GAP domain
ComponentsADP-ribosylation factor GTPase-activating protein GLO3
KeywordsPROTEIN TRANSPORT / ArfGAP domain / GTPase activating protein domain / membrane trafficking / COPI
Function / homology
Function and homology information


COPI coating of Golgi vesicle / COPI-coated vesicle / COPI vesicle coat / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / endoplasmic reticulum to Golgi vesicle-mediated transport / GTPase activator activity / protein transport / Golgi membrane / metal ion binding
Similarity search - Function
Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger
Similarity search - Domain/homology
ADP-ribosylation factor GTPase-activating protein GLO3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsXie, B. / Jackson, L.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM119525 United States
CitationJournal: Adv Biol Regul / Year: 2021
Title: The Glo3 GAP crystal structure supports the molecular niche model for ArfGAPs in COPI coats.
Authors: Xie, B. / Jung, C. / Chandra, M. / Engel, A. / Kendall, A.K. / Jackson, L.P.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 24, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: ADP-ribosylation factor GTPase-activating protein GLO3
A: ADP-ribosylation factor GTPase-activating protein GLO3
C: ADP-ribosylation factor GTPase-activating protein GLO3
D: ADP-ribosylation factor GTPase-activating protein GLO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,41910
Polymers70,9734
Non-polymers4466
Water2,666148
1
B: ADP-ribosylation factor GTPase-activating protein GLO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9013
Polymers17,7431
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
A: ADP-ribosylation factor GTPase-activating protein GLO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8092
Polymers17,7431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: ADP-ribosylation factor GTPase-activating protein GLO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,8092
Polymers17,7431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: ADP-ribosylation factor GTPase-activating protein GLO3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9013
Polymers17,7431
Non-polymers1582
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.369, 74.031, 77.902
Angle α, β, γ (deg.)90.000, 105.344, 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

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Components

#1: Protein
ADP-ribosylation factor GTPase-activating protein GLO3 / ARF GAP GLO3


Mass: 17743.281 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: GLO3, YER122C / Production host: Escherichia coli (E. coli) / References: UniProt: P38682
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 148 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.38 % / Description: needle/blade shape
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 2.0 M ammonium sulfate, 0.1 M sodium acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.77118 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 22, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77118 Å / Relative weight: 1
ReflectionResolution: 2.07→41.2017 Å / Num. obs: 34082 / % possible obs: 93.55 % / Redundancy: 2 % / Biso Wilson estimate: 37.55 Å2 / Rrim(I) all: 0.11 / Net I/σ(I): 13
Reflection shellResolution: 2.07→2.14 Å / Num. unique obs: 34082 / Rrim(I) all: 0.11

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
Cootrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2P57

2p57


Resolution: 2.07→41.2 Å / SU ML: 0.3281 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29.2325
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2381 1678 4.98 %
Rwork0.1811 32021 -
obs0.1839 33699 92.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.45 Å2
Refinement stepCycle: LAST / Resolution: 2.07→41.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4500 0 16 148 4664
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00734598
X-RAY DIFFRACTIONf_angle_d0.88166187
X-RAY DIFFRACTIONf_chiral_restr0.0497688
X-RAY DIFFRACTIONf_plane_restr0.0057785
X-RAY DIFFRACTIONf_dihedral_angle_d16.42761721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.07-2.130.45061300.44072490X-RAY DIFFRACTION86.87
2.13-2.20.31151480.30712822X-RAY DIFFRACTION98.87
2.2-2.280.3958970.31691897X-RAY DIFFRACTION66.05
2.28-2.370.2691410.23042853X-RAY DIFFRACTION98.88
2.37-2.480.24251600.20372782X-RAY DIFFRACTION97.55
2.48-2.610.27431410.19492701X-RAY DIFFRACTION93.89
2.61-2.770.27171450.19632745X-RAY DIFFRACTION95.95
2.77-2.990.27461570.1992873X-RAY DIFFRACTION99.7
2.99-3.290.25791420.18272869X-RAY DIFFRACTION99.54
3.29-3.760.22081350.1652515X-RAY DIFFRACTION87.4
3.76-4.740.1871280.1292503X-RAY DIFFRACTION86.46
4.74-41.20.19451540.14852971X-RAY DIFFRACTION99.78
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)
14.05287170864-4.28225912643.209059503164.57942448937-3.393751678142.576219944161.074842060790.407370198960.320046403311.23227540599-1.67841925494-0.590915489292-0.4269399439360.5392461829140.9016165499210.788848327105-0.0828518396526-0.1485861673530.651747512659-0.1453164795760.74086318492426.518908224728.577851092440.7477662045
28.404047531.392271346344.936160161482.395781226921.502206073138.519403815040.203671340201-1.864396712920.7470460786411.614518061410.01339174389140.807241779056-1.14153057543-0.942838826403-0.08808033997150.653958903715-0.0397070674050.1417848997080.513306256046-0.1126176042640.49771236447810.631821000624.664972706442.7785138103
32.35779479427-0.4709977368570.3333090005482.348160871790.4187901372427.524592833120.148855471566-0.365715870696-0.1797832717750.176967532680.3470773557240.990387495225-0.0376480123427-0.586710101126-0.4862860326820.40665844451-0.0958982179513-0.01919747272010.4573498910470.1067431931410.4993147077896.1892839547810.837824571237.1588703228
49.58794069123.97042765667-1.772144913759.60964011946-0.8090295094616.767512868990.209532002161-0.391650545438-0.2197471792020.665869415134-0.1424413176350.102644257150.120135020528-0.0515616545757-0.01915699079260.281865784471-0.0369912508096-0.05303037383510.209987297569-0.01890483971760.2235130627516.198762763312.621686120436.1721298927
57.112640460234.55513806289-3.994135482076.28704243622-0.4484835899635.219551764310.0714764992675-0.170541451893-0.750203873638-0.124691691228-0.262329560156-0.686826597191-0.05897515962880.003272939444950.2644496541510.2885127532610.0335081341251-0.05022454730330.3529180924140.1075657698950.3831710671721.68078328177.2891405031836.6268396394
66.52280446487-0.7730865638690.5285197171159.31844687734-1.400266649926.83520864360.0601536303387-0.963001613079-0.1556931133320.8088330478940.107951436009-0.310244403161-0.493867113511-0.00524161180008-0.1332036850190.336446100079-0.06333822010140.013151280750.326617882057-0.01199606463860.20523710320618.679188243421.882643366938.5939875036
75.664457943760.442912332121-2.903996360746.225202945494.919319949298.02950899068-0.4623855270180.3630761697210.0191623241225-1.237768220740.1204545492921.41202788121-0.562226180045-0.7991617125440.4197491843580.390434960299-0.0762358278956-0.1678329693110.3785124178890.07461187719740.3901337965127.8338664336715.122020467524.5381015092
84.180944341872.98205124777-3.751204780692.61854431534-4.011815704138.00661486637-0.104560484733-0.0604968402858-1.70871530783-1.557908101050.4067707680660.4587948690250.759625261755-0.724000094004-0.3423325131310.598420647549-0.0765952022545-0.1535240788270.3765479159770.006970418522910.65006537702412.68744788864.0084095586124.7422665951
97.461129649632.370365682121.071311146442.909196196224.095011644267.69737787187-0.3106477838870.4243020390240.594473173588-0.6202456095350.559165502452-0.105060751272-0.08371502833050.233244424506-0.2385242118770.354704052611-0.0570355118070.01442263690020.2213989433550.01199301325750.22295911995419.663859568222.010851284224.3989837019
105.981738022785.70160736383-5.972682672415.84429308329-6.256292722186.79504091254-0.378767436841-1.01286590791.150962897820.7440818370390.7972977390520.611099333603-0.165292733885-0.544488533379-0.5007153173240.643997555483-0.01167764119240.1041702822350.353820706839-0.1050081900910.55490219581217.127204765133.213527074835.6160250216
113.907118747961.759803531073.788719811718.51562349081-0.4112857212024.37341639804-0.2220179785930.3362581050480.692397858513-0.638208627987-0.197571865692-0.0757211228901-0.341703271104-0.2935348928760.4684597066680.4606313264140.09420972300150.01059969454890.429465933926-0.03413202216690.33342682388137.97007540820.087394284514.4181739806
125.90594149393-0.5764357033380.309500463876.12873529531-0.2991966397845.86896650268-0.01684082411690.197651739832-0.383159063658-0.5152738074530.05152866317280.05087159015290.2658935698670.02159940922650.009596873513520.2667649495480.0194393679612-0.02338871602450.253800534706-0.04354092456990.28639872038745.16397167425.3821084692518.183942999
135.63622940523-4.90432340129-0.5664100190168.13848102633-3.352218889453.899191208850.0672086744262-0.1854182002570.3814906516720.196032025271-0.0923472263873-0.3440345332620.0319876028976-0.2804118446190.04752351460740.194489048048-0.01827052466820.00968751485230.2094560635-0.06886088572460.2723942613141.146698925813.216210321123.493050863
148.167597481593.78827972486-2.080887480122.46592408921-2.653890853836.40001854603-0.607391249797-0.757402911216-1.792816927190.7745577311170.495836452744-0.9972088752240.7989386906150.8138695377080.1517215258680.5690298320080.140149611777-0.101134337510.432348034920.009007775024680.74971135040250.3115907573-0.96387448633528.9116848674
155.08325051046-5.134650137163.448840366715.28481072417-4.275243735157.05520672512-0.759804532689-1.245363546080.1007091227810.7369676882670.7313197536680.023804388820.0430741004832-0.187316255606-0.006022851595320.3444620461170.06090026930060.07171746088320.3706560184960.05818973125730.47325182798836.092223109811.909258823432.6509256769
162.39152976715-2.36077761192-2.814521854789.619739027821.846349291216.03678472118-0.101311342171.029190300811.29968309836-0.696259893940.466720583688-0.342760174557-0.7789960062170.0596521843414-0.4023953443930.3716468632690.08138021751030.1642160048640.520223314734-0.05327965868760.55775102198231.968155984725.020162410323.9817822291
178.251442753590.00484690611312-6.665222344682.758264544061.610751871538.964362083570.324002341687-0.9626399894181.267241177750.5533414703610.188429854393-0.06590986869750.4751611001560.208388922727-0.7298453228010.457048990155-0.07786547728010.005386465025660.4755862584050.03367902913830.54138493454432.847754618516.807035093879.1480980295
185.336852995751.62183876424-2.199276435555.57569355582-0.9862739771273.97885594390.0346768261863-0.1588849948220.604336326538-0.07818154058720.1297495345330.12649773556-0.330712072332-0.18351592905-0.154669364910.3335864917570.0305569398463-0.004329844628320.308733415973-0.05482162505760.43078228721137.363816439921.304898739167.082915253
199.79781572914-1.29900213766-1.177536756122.27418967509-0.2736878549049.46632191774-0.1344454886130.654055702373-0.409720317898-0.632026611665-0.204119697102-0.2779770808310.8265409735850.3540993340950.4463264358390.4595463914480.03027216235480.07939830240940.361340357809-0.07422498335160.49751425615144.73346227429.5630740400358.1196923138
203.00359358917-2.889286680371.792011031133.60231422946-3.418812977826.400748225030.1438956467972.053551919511.05326408844-0.279690334831-0.310827231532-1.002687230270.3221860123080.3116618570920.2087355912040.4802007258780.000606396664194-0.0267303511870.568598502350.1305064813230.51178892909343.698651190920.627315714353.5054099624
217.760846593655.43536091362-6.116932546624.51268536393-4.782852411065.12248948642-0.6765502584950.925632991153-0.790010530089-0.4901601435390.8609718612330.2252394287390.955460634964-1.40796799813-0.3001055158010.4178413897-0.0961117645795-0.006259096925620.4644249219070.006708441409110.59756518287730.34794769837.486720090861.828787151
225.659233796434.166266017545.066128515883.123571718113.753182806884.551381230370.293340835397-1.87775014064-2.053652960092.065005987090.111527097739-0.9274546230070.08052677456410.707434382275-0.2666820195190.5676524663980.0179911182464-0.05629884882040.7489500963050.1480318133040.69653983830127.29088596616.2666353580177.3168763883
232.66599055557-4.720719839131.699049561649.91277492166-0.9294097485128.877301015510.192709004608-0.0416608397739-1.104230388510.406962189593-0.2624300504980.6846278676641.15403386788-0.01961487259410.08879808955810.4696495488390.02128032718270.004059819780360.299210874584-0.06551491729450.6028701499257.9952222683-8.8282366746566.8310822135
245.8122141471-3.037510389981.239428189128.261743777940.7663080972147.341759032110.4029645018650.5082560419910.322973136092-1.06769157987-0.4845147694810.169001391076-0.263244044072-0.1872473651070.08442202196220.3736847650660.0876751502490.00344378813830.332017986711-0.04302335360320.3015125778119.880020895243.2633461225257.9308501764
255.91792493119-3.326384797642.123432918552.68974528999-1.085116536444.20542779162-0.259571944314-0.3511083395020.2996916517020.760011304490.1119172527290.372248551741-0.135540778729-0.1877932562660.1002072442440.3047213452140.001861270039330.01028336980330.222752955931-0.03510912430140.3268067005257.45785912325.7407677652169.5095897095
266.513295008872.224022132814.183800984033.267900841853.838193978485.00966244621-0.3188931396871.60949800791.99019877356-0.83036491459-0.4742550824520.515474553024-2.201363049360.1761948259841.01155397350.7402839832140.0966954595617-0.08037909673520.4863105534330.04224897156470.7482579360193.7097682543518.811927856859.1572070113
275.3531636082-4.911589685952.143366568589.46650063329-0.7995228276266.59716528355-0.311235191377-0.5079708649860.4260490851570.7390673399180.247247610517-0.619667881913-0.509589321242-0.1909347107890.08724608630280.2554319202540.00619440829258-0.09708511808510.32666780615-0.03433142999590.40982019624213.36074390476.5555466415972.2798552564
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 11 )
2X-RAY DIFFRACTION2chain 'B' and (resid 12 through 24 )
3X-RAY DIFFRACTION3chain 'B' and (resid 25 through 40 )
4X-RAY DIFFRACTION4chain 'B' and (resid 41 through 51 )
5X-RAY DIFFRACTION5chain 'B' and (resid 52 through 70 )
6X-RAY DIFFRACTION6chain 'B' and (resid 71 through 88 )
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 98 )
8X-RAY DIFFRACTION8chain 'B' and (resid 99 through 118 )
9X-RAY DIFFRACTION9chain 'B' and (resid 119 through 138 )
10X-RAY DIFFRACTION10chain 'B' and (resid 139 through 146 )
11X-RAY DIFFRACTION11chain 'A' and (resid 7 through 24 )
12X-RAY DIFFRACTION12chain 'A' and (resid 25 through 70 )
13X-RAY DIFFRACTION13chain 'A' and (resid 71 through 98 )
14X-RAY DIFFRACTION14chain 'A' and (resid 99 through 118 )
15X-RAY DIFFRACTION15chain 'A' and (resid 119 through 138 )
16X-RAY DIFFRACTION16chain 'A' and (resid 139 through 145 )
17X-RAY DIFFRACTION17chain 'C' and (resid 7 through 24 )
18X-RAY DIFFRACTION18chain 'C' and (resid 25 through 88 )
19X-RAY DIFFRACTION19chain 'C' and (resid 89 through 104 )
20X-RAY DIFFRACTION20chain 'C' and (resid 105 through 118 )
21X-RAY DIFFRACTION21chain 'C' and (resid 119 through 138 )
22X-RAY DIFFRACTION22chain 'C' and (resid 139 through 146 )
23X-RAY DIFFRACTION23chain 'D' and (resid 8 through 24 )
24X-RAY DIFFRACTION24chain 'D' and (resid 25 through 77 )
25X-RAY DIFFRACTION25chain 'D' and (resid 78 through 98 )
26X-RAY DIFFRACTION26chain 'D' and (resid 99 through 111 )
27X-RAY DIFFRACTION27chain 'D' and (resid 112 through 146 )

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