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- PDB-6pta: Crystal structure of the ARF family small GTPase ARF1 from Candid... -

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Basic information

Entry
Database: PDB / ID: 6pta
TitleCrystal structure of the ARF family small GTPase ARF1 from Candida albicans in complex with GDP
ComponentsADP-ribosylation factor
KeywordsSIGNALING PROTEIN / GTPASE / GDP / GTP / ARF FAMILY / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport / GTP binding / Golgi apparatus / plasma membrane
Similarity search - Function
small GTPase Arf family profile. / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Joachimiak, A. / Satchell, K.J.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201700060C United States
CitationJournal: To Be Published
Title: Crystal structure of the ARF family small GTPase ARF1 from Candida albicans in complex with GDP
Authors: Stogios, P.J.
History
DepositionJul 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 24, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 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
A: ADP-ribosylation factor
B: ADP-ribosylation factor
C: ADP-ribosylation factor
D: ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8908
Polymers81,1174
Non-polymers1,7734
Water1,964109
1
A: ADP-ribosylation factor
C: ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4454
Polymers40,5592
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2670 Å2
ΔGint-25 kcal/mol
Surface area15690 Å2
MethodPISA
2
B: ADP-ribosylation factor
D: ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4454
Polymers40,5592
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2680 Å2
ΔGint-25 kcal/mol
Surface area15950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.801, 42.285, 90.343
Angle α, β, γ (deg.)90.000, 93.699, 90.000
Int Tables number3
Space group name H-MP121
Space group name HallP2y
Symmetry operation#1: x,y,z
#2: -x,y,-z

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Components

#1: Protein
ADP-ribosylation factor


Mass: 20279.262 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (strain SC5314 / ATCC MYA-2876) (yeast)
Strain: SC5314 / ATCC MYA-2876 / Gene: ARF1, CAALFM_CR08700CA, CaO19.13805, CaO19.6447 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): -Gold / References: UniProt: P22274
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.2 M ammonium Acetate, 30% PEG 4K, 0.1M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. obs: 22742 / % possible obs: 98.5 % / Redundancy: 3.2 % / Biso Wilson estimate: 42.53 Å2 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.076 / Net I/σ(I): 8.61
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.834 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 1081 / CC1/2: 0.798 / Rpim(I) all: 0.533 / % possible all: 97

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Processing

Software
NameVersionClassification
PHENIX1.15_3448refinement
PHENIX1.15_3448refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R8Q

1r8q


Resolution: 2.5→24.5 Å / SU ML: 0.3309 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 44.1369
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 1133 5.02 %RANDOM
Rwork0.2573 ---
obs0.2594 22574 97.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 57.43 Å2
Refinement stepCycle: LAST / Resolution: 2.5→24.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5336 0 0 109 5445
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00525428
X-RAY DIFFRACTIONf_angle_d0.78217370
X-RAY DIFFRACTIONf_chiral_restr0.0501844
X-RAY DIFFRACTIONf_plane_restr0.0035914
X-RAY DIFFRACTIONf_dihedral_angle_d19.64651984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.610.37421350.34212584X-RAY DIFFRACTION95.3
2.61-2.750.36061440.33972648X-RAY DIFFRACTION97.59
2.75-2.920.40341370.31692674X-RAY DIFFRACTION98.32
2.92-3.150.31871310.2982670X-RAY DIFFRACTION98.28
3.15-3.460.30211390.26892730X-RAY DIFFRACTION98.76
3.46-3.960.31041480.23292700X-RAY DIFFRACTION99.13
3.96-4.990.25761480.21072755X-RAY DIFFRACTION99.28
4.99-24.50.24791510.22612680X-RAY DIFFRACTION93.9
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)
14.06501459871-1.22012254669-1.106860754975.98440118184-3.429727211387.276914800370.688834030037-0.5801058992680.5784295335050.104196868811-0.9496738887010.0384460575354-0.8078168509780.05040012650820.3261311739440.477235135115-0.0743009796093-0.03058362798130.515563419401-0.1359425142240.32887990458727.284785515321.46107805084.53703224936
21.695483175420.579372029261-1.680693368394.77766141133-0.2545942535286.836714863660.50726792109-1.086472701250.3573866694770.398709352689-0.1957504687270.532937566011-0.2510789644110.639999199734-0.233897457450.464256771608-0.1853816841320.0008684057925760.667831711379-0.01842807920210.36064033166930.843319081624.488703644711.4846696049
39.22705460698-6.413502298924.205890249998.22627822894-2.725648520834.0221397979-0.660282665939-0.6178806695910.2117182582610.5099098302070.3492639955580.720344070592-0.666109624739-1.40845434420.3277686828670.61150572329-0.1002667915470.01573813096750.756717614293-0.05175738316770.72585371239918.113088682621.56352824417.0562281727
44.86848630047-1.79886341904-0.4516545134164.993703709660.1982950925283.108044912320.1955488203790.704381581311-0.321807260192-0.253959550843-0.5039750771250.108084087244-0.0358944447533-0.1484106987450.2741186918720.389749312791-0.00457128846693-0.08262245231370.645570071080.05616350803760.34566449857424.04966632689.552448127954.2099874265
50.3480219223060.3890916117470.3152004458171.22469391010.3839369878170.286189694845-0.43972766209-0.4949835496820.787212712051-1.31013089626-0.238691622155-1.097604233370.8500398638630.7647802673030.6294225503241.08769947601-0.4073753379710.6007846566561.12410386968-0.1884570749621.2416648339515.068076233823.2887005353-4.2705192592
62.33109770445-2.47526795104-3.326057851054.280884525452.746462892198.250997736650.04303552870791.356010868580.48199216661-0.586170078582-0.0440925713557-1.039910955940.2041127651720.6110696136050.1620311395571.03201719930.0441203596650.03346789494321.052704701410.283295786480.38155255097813.253250230448.509691807747.7231206841
71.81464218422-1.552695930981.141123995691.67799355163-1.495893968082.50834805899-0.495353553257-0.670642012080.3548889589320.483135708207-0.145231460196-0.2918984122690.014929033794-0.4576553445460.2596076904730.0993086645291-0.2793424777650.1054582514980.1505746565860.07687770936670.63307195705810.363125891543.997312956633.7076596704
89.766745504831.90777162385-0.6994628525225.01384957585-0.394948899153.16270377386-0.1889013198551.214817420181.3086939227-1.218693283181.03586181409-0.328968418636-0.8631124357880.703869523851-1.078509917040.654398496825-0.1651666063750.07770705023810.801693036238-0.02590839082210.36938761609622.333321378142.706874834227.8191308771
95.669976029040.635367466839-1.466563878543.70628554723-0.1361224561843.64568516783-0.3026563820820.229854783689-0.07719136479280.3285560098650.54739629263-0.2313087771810.3576272074470.497196549003-0.2083563940210.3689412397950.0876604220443-0.03128864689870.2628146518810.0447955253340.2361318613816.441018976830.668997571940.8612449239
103.66166225743.371940077482.562019973534.910810290692.797242711972.213509276820.42912885969-0.6589323122810.2577508494720.831767389956-0.0642610361426-0.8590695048540.50771548611-0.368569158982-0.3158645682950.54916725154-0.260231131658-0.2732434055161.18709918756-0.1685217362770.67000440970825.490335353244.493308200549.4485762616
114.88534767631-1.91438053529-1.954246363057.08895666939-0.3329542614347.50257776884-0.06478796140930.0737697058852-0.2091509621610.8093466413880.0509456124932-0.731251253171-0.607752466290.892116061711-0.07844016979520.3147255460580.070999129567-0.04036993512320.555907402173-0.1452961648630.44094235008546.54503209731.92689776527.7416551485
125.94727029182-2.87655687052-0.1253583088983.838389685461.860995796552.4966174285-0.412254562961-0.3390517839480.0312069854069-0.04635150181250.03278706486650.318231168918-0.08220858858021.071594636410.5303321370530.5049313832930.0254169180563-0.05233699511710.5300672812010.0955533222040.52543896061842.380528664226.293134544420.1564632884
131.142277244940.452252849211-1.288652161621.92712687429-1.93288344034.81963655522-0.2385616298620.637513992824-0.146890805966-0.8211403711870.539688631324-0.838240591049-0.7130023989310.39176472947-0.3921990666360.9882945423370.3152741340710.1168778272721.63487863565-0.3784720621430.61641985359456.36080169522.462926059915.9779904829
147.043955902112.10879105307-0.7703949117884.81368160421-1.274516804764.776505166620.06256647472341.06644497098-0.546565750278-0.511470376353-0.0454435870807-0.5613763057131.135592518740.4356010059430.04485774031720.376328073865-0.0184862299105-0.1358673410390.525991878139-0.1080575511220.427906757650.900216502216.682619573633.2216559801
155.78600860305-0.594896096443-0.1131665550684.986436979-2.788768655672.575192654110.4919482899290.662470168571-0.4482703963421.04814185465-0.129476722953-0.1645508640430.05911812847050.0908482662237-0.2358956704320.3232636980280.0378812526873-0.151984434020.754299250404-0.1449369724860.33273680081645.29428270328.184254050837.1490860273
162.94303327932.896823385265.838828896311.999950499052.000084976661.99991140588-0.130834830619-0.2714957046150.497758104782-3.123206239741.13907476208-1.44778983889-2.675624708871.11535624344-0.9931420750090.975099020116-0.4280096890150.2588070396980.829909068065-0.1731972072340.4718091355454.376765159236.644786865831.0460126989
177.695410906952.17960493399-2.10164170478.82128634542-1.465750687196.51030983159-0.2024499312840.07157002228441.107967968-0.520679929055-0.2234462524380.175961523817-0.312364209804-0.3938551312420.4366262270080.4961827952430.156589399507-0.1931516885120.3984095418560.03044219385530.259721054573-6.2322185774454.413789934117.4864439974
187.019071110543.50275870552-2.550147541545.37017579242-1.183237429627.778607052690.751683175868-1.011181596910.9143388830140.61319926841-0.323116636660.605728073157-0.4458433332980.677000652998-0.4144718139210.2511895223410.108765940673-0.0241616899450.5322550660330.08627335902560.272111444005-1.8231272378447.376038247824.8288491275
197.17042003331.88757393329-1.086326738035.517335867051.139877195874.08009720130.769229649893-2.232728319390.320086054731.271269716850.2812450939180.208353166140.113599704994-0.516095745412-0.887986445510.6903367544950.1315398798330.1425086495071.07934331621-0.01286720654640.337929041383-14.458279367340.980556059629.5432241648
206.05581605265-2.489456098663.211614934536.9144281877-4.141765548243.97451133293-0.197115836263-0.655376109955-0.6100556943821.11238992909-0.06613361110670.32490742660.817817081278-1.01912446070.2860425707540.657797217221-0.279562984781-0.01318418543610.408691833352-0.1295123375540.425429962016-11.727356629445.458534814119.0642765183
216.98323806288-3.558734478040.2803426395925.13003617379-1.322805253842.88730620898-0.001083028701670.164042421556-0.783737181246-0.2424978340320.0211513603070.4615915977040.823632994132-0.7230036101210.04162000189230.614305435604-0.212296393759-0.005207588578870.59779289472-0.05346948826150.50079404727-10.636883387537.035537096411.1822661037
221.00190649379-1.20539344580.7795805410382.162221518380.4104455657673.159856245910.5585473239250.09649948289530.4435334756040.1098101742170.004541041924260.323504997647-0.3139319371370.354833213395-0.2946628996160.605131098757-0.011580999140.2723689502450.1910691826970.155751792470.505657464338-2.2132271573645.11607097567.21867783313
233.045901021120.9515235830543.846498642476.30697007882-2.526251363347.16426586202-0.3589883421330.2764334902320.519705072096-0.3931633001320.14060926221-0.6053759862170.480427227218-0.6497935517230.2639236039840.661459342157-0.04906751097590.2021120864810.42963347488-0.01528998215520.507350805077-7.4859271623153.49159317838.60008729042
245.499844486465.252877025213.752575946981.99995810366-7.941074558881.99990731719-3.24458050727-0.5707907533251.030635483567.17346404632.64842003429-2.14795395777-4.67004500663-2.101818729520.8299479615651.21919597542-0.150555998336-0.112249935261.00771375156-0.3408634927680.480051742072-14.575128270158.662765662913.9069184096
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 29 )
2X-RAY DIFFRACTION2chain 'A' and (resid 30 through 67 )
3X-RAY DIFFRACTION3chain 'A' and (resid 68 through 84 )
4X-RAY DIFFRACTION4chain 'A' and (resid 85 through 176 )
5X-RAY DIFFRACTION5chain 'A' and (resid 177 through 179 )
6X-RAY DIFFRACTION6chain 'B' and (resid 8 through 18 )
7X-RAY DIFFRACTION7chain 'B' and (resid 19 through 67 )
8X-RAY DIFFRACTION8chain 'B' and (resid 68 through 84 )
9X-RAY DIFFRACTION9chain 'B' and (resid 85 through 176 )
10X-RAY DIFFRACTION10chain 'B' and (resid 177 through 179 )
11X-RAY DIFFRACTION11chain 'C' and (resid 8 through 25 )
12X-RAY DIFFRACTION12chain 'C' and (resid 26 through 68 )
13X-RAY DIFFRACTION13chain 'C' and (resid 69 through 84 )
14X-RAY DIFFRACTION14chain 'C' and (resid 85 through 152 )
15X-RAY DIFFRACTION15chain 'C' and (resid 153 through 176 )
16X-RAY DIFFRACTION16chain 'C' and (resid 177 through 178 )
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 24 )
18X-RAY DIFFRACTION18chain 'D' and (resid 25 through 67 )
19X-RAY DIFFRACTION19chain 'D' and (resid 68 through 81 )
20X-RAY DIFFRACTION20chain 'D' and (resid 82 through 93 )
21X-RAY DIFFRACTION21chain 'D' and (resid 94 through 152 )
22X-RAY DIFFRACTION22chain 'D' and (resid 153 through 165 )
23X-RAY DIFFRACTION23chain 'D' and (resid 166 through 176 )
24X-RAY DIFFRACTION24chain 'D' and (resid 177 through 178 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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