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- PDB-5uf8: Crystal structure of the ARF family small GTPase ARF2 from Candid... -

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Basic information

Entry
Database: PDB / ID: 5uf8
TitleCrystal structure of the ARF family small GTPase ARF2 from Candida albicans in complex with GDP
ComponentsPotential ADP-ribosylation factor
KeywordsSIGNALING PROTEIN / Signalling 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


filamentous growth / vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus / plasma membrane
Similarity search - Function
ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases ...ADP-ribosylation factor 1-5 / Small GTPase superfamily, ARF type / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / 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: 1.872 Å
AuthorsStogios, P.J. / Skarina, T. / Di Leo, R. / Savchenko, A. / Anderson, W.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)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of the ARF family small GTPase ARF2 from Candida albicans in complex with GDP
Authors: Stogios, P.J.
History
DepositionJan 3, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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: Potential ADP-ribosylation factor
B: Potential ADP-ribosylation factor
C: Potential ADP-ribosylation factor
D: Potential ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,1478
Polymers82,3744
Non-polymers1,7734
Water9,566531
1
A: Potential ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0372
Polymers20,5931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Potential ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0372
Polymers20,5931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Potential ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0372
Polymers20,5931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Potential ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,0372
Polymers20,5931
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)38.289, 64.362, 79.236
Angle α, β, γ (deg.)78.11, 83.73, 72.77
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Potential ADP-ribosylation factor


Mass: 20593.467 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: ARF2, orf19.5964, CaO19.13385, CaO19.5964 / Plasmid: pMCSG68SBPTEV / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold / References: UniProt: Q5AND9
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 531 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 30% PEG2K MME, 0.2 M ammonium sulfate, 0.1 M sodium acetate pH 4.6, 5 mM magnesium chloride, 5 mM ADP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.88→25 Å / Num. obs: 53906 / % possible obs: 93.4 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.054 / Net I/σ(I): 41.35
Reflection shellResolution: 1.88→1.91 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 5.04 / CC1/2: 0.838 / % possible all: 90.7

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Processing

Software
NameVersionClassification
PHENIX(dev_2481: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
BALBESphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MR3

1mr3


Resolution: 1.872→24.873 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.1 / Phase error: 29.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2698 1950 3.72 %RANDOM SELECTION
Rwork0.235 ---
obs0.2364 52456 90.14 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.872→24.873 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5154 0 112 531 5797
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035373
X-RAY DIFFRACTIONf_angle_d0.6477313
X-RAY DIFFRACTIONf_dihedral_angle_d19.3941985
X-RAY DIFFRACTIONf_chiral_restr0.046829
X-RAY DIFFRACTIONf_plane_restr0.003916
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8715-1.91830.26141110.2552930X-RAY DIFFRACTION74
1.9183-1.97020.32651340.26873382X-RAY DIFFRACTION85
1.9702-2.02810.31681380.25583520X-RAY DIFFRACTION87
2.0281-2.09350.33441320.25583477X-RAY DIFFRACTION88
2.0935-2.16830.30191370.26263590X-RAY DIFFRACTION89
2.1683-2.25510.29871400.25153605X-RAY DIFFRACTION90
2.2551-2.35760.31261390.26583594X-RAY DIFFRACTION90
2.3576-2.48180.31011420.25063679X-RAY DIFFRACTION91
2.4818-2.63720.29661410.25273666X-RAY DIFFRACTION92
2.6372-2.84050.28461450.25683698X-RAY DIFFRACTION93
2.8405-3.12590.32011460.25393789X-RAY DIFFRACTION94
3.1259-3.5770.24291470.22253817X-RAY DIFFRACTION95
3.577-4.50230.21081480.20463843X-RAY DIFFRACTION96
4.5023-24.8750.25431500.21783916X-RAY DIFFRACTION98
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)
19.7282-0.26164.72957.074-1.71762.65790.4849-0.2799-0.82340.42320.3964-0.88750.9519-0.0227-0.77790.30590.0229-0.05570.3652-0.01210.43987.3037-1.14489.9736
21.42520.27920.16413.64820.67733.47560.0361-0.04380.18730.0560.0040.03740.0945-0.0297-0.04980.1857-0.0284-0.00320.2539-0.00860.25724.31878.64634.6644
36.48291.3865-6.72012.1246-1.62827.0148-0.06911.8411-0.6238-0.5771-0.3950.6669-0.402-0.66490.41310.4787-0.0419-0.01450.6919-0.17520.671915.01045.0695-7.9592
43.14280.0306-1.07927.1899-3.83563.16-0.4689-0.4517-0.20340.66660.5035-0.8524-0.2382-0.2273-0.02280.4141-0.1608-0.1020.592-0.0510.402815.9197-0.4222.469
53.3423-0.55840.64873.9002-0.99222.88310.010.2785-0.0981-0.3516-0.0349-0.16620.308-0.04120.0160.2507-0.04120.02270.2567-0.01050.2576-1.0855-3.0739-6.7857
62.0043-0.4879-0.31865.2082-0.54774.33690.0142-0.1196-0.01180.1772-0.03710.01860.478-0.2125-0.02160.2539-0.05750.02930.25350.03140.2894-6.8374-4.00334.2265
75.92690.72861.74032.559-1.6736.9727-0.2622-0.49240.13040.39370.09320.153-0.8117-0.18620.16380.2723-0.0011-0.00650.18470.01650.293-11.144-34.69711.277
82.30381.97880.7992.7184-0.79062.0364-0.0156-0.0020.32530.13940.02180.0424-0.2638-0.091-0.04330.35680.02370.00580.2535-0.04070.255-16.2684-40.46915.7033
97.15961.07960.82748.35424.5053.1403-0.76340.11760.13490.50330.11150.6231-0.19451.05520.55470.3163-0.09070.04080.22810.03610.3256-15.8082-33.71783.799
103.4907-3.5050.13398.9011-6.69318.0933-0.32-0.6645-0.03361.4561.30760.478-0.8656-2.3196-0.61130.44560.11460.07570.80160.01670.614-25.4618-29.85544.1411
113.71260.7438-1.16253.3289-0.32068.0543-0.02290.26960.1998-0.19310.09640.21630.3134-0.2421-0.06620.2755-0.0238-0.00080.18640.02420.3375-14.1853-29.6924-10.4382
122.7168-0.27810.78675.9863-0.76975.6541-0.1385-0.04780.14630.1213-0.0514-0.0643-0.52430.02020.18970.2052-0.0681-0.00480.20460.00190.272-7.789-24.5746-5.5957
136.74754.9396-4.8126.9221-5.03094.19570.01180.42630.1024-0.5709-0.3906-0.18060.2770.65640.45560.31150.14580.01920.45440.08760.322714.628818.210431.6097
144.6703-0.95340.79713.48061.04782.99160.06610.3247-0.0114-0.14390.0225-0.2275-0.31690.0901-0.0780.21580.01990.00270.20910.0240.24413.07489.843833.7069
155.19193.9965-2.58784.2179-1.32032.35220.2332-0.44240.1123-0.0096-0.9487-0.3237-0.51110.39510.7110.39310.19510.01170.6233-0.08590.566324.980115.149642.1317
164.63670.3937-2.8773.1536-3.22188.70920.0151-0.51560.36580.0921-0.2785-0.4425-0.32950.75050.25810.23630.0372-0.02890.2512-0.00610.33112.629720.413744.2744
176.32241.58210.19936.34490.33451.53540.1467-0.24760.51770.818-0.11520.2039-0.2571-0.238-0.00260.31880.088-0.02830.32430.03590.23242.463420.898343.9557
182.68790.5228-0.884.72610.11652.0536-0.00720.15050.24940.00030.12050.0937-0.382-0.309-0.10150.25720.0636-0.00980.27370.02730.23482.899924.490636.922
198.7572-3.1843-0.26832.8658-3.94519.49710.30491.1003-1.7206-2.9871-0.60881.16960.9136-0.13260.35691.1651-0.059-0.24590.4913-0.10310.87731.063544.445723.5721
203.0090.04332.08943.8252-2.4393.3485-0.02260.1983-0.1602-0.1915-0.0227-0.08860.10520.06950.04240.20690.03370.0120.281-0.02980.269733.402955.918834.1086
214.1423-1.43512.22812.438-1.5851.5355-0.16340.9191-0.4728-0.4679-0.34221.7180.2287-1.05780.22770.327-0.0195-0.0870.8929-0.19690.825122.468248.542834.8947
223.4850.36260.34362.03640.82228.5450.0254-0.3792-0.18530.13550.06260.005-0.37890.0652-0.10360.28870.03760.0050.1935-0.01270.404432.814948.860250.122
231.7688-1.09280.34444.79160.01097.1785-0.0797-0.1525-0.07830.1607-0.0470.343-0.0024-0.54760.11420.22150.05420.01030.1950.00460.364236.52444.655546.7425
242.1056-0.1234-1.46364.3193-0.35454.896-0.21440.3258-0.0176-0.22380.0328-0.00510.4227-0.06150.19090.24270.05780.01930.2562-0.00110.383441.579541.770940.438
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 17:21 )A17 - 21
2X-RAY DIFFRACTION2( CHAIN A AND RESID 22:68 )A22 - 68
3X-RAY DIFFRACTION3( CHAIN A AND RESID 69:77 )A69 - 77
4X-RAY DIFFRACTION4( CHAIN A AND RESID 78:84 )A78 - 84
5X-RAY DIFFRACTION5( CHAIN A AND RESID 85:149 )A85 - 149
6X-RAY DIFFRACTION6( CHAIN A AND RESID 150:177 )A150 - 177
7X-RAY DIFFRACTION7( CHAIN B AND RESID 17:36 )B17 - 36
8X-RAY DIFFRACTION8( CHAIN B AND RESID 37:56 )B37 - 56
9X-RAY DIFFRACTION9( CHAIN B AND RESID 57:72 )B57 - 72
10X-RAY DIFFRACTION10( CHAIN B AND RESID 75:84 )B75 - 84
11X-RAY DIFFRACTION11( CHAIN B AND RESID 85:109 )B85 - 109
12X-RAY DIFFRACTION12( CHAIN B AND RESID 110:177 )B110 - 177
13X-RAY DIFFRACTION13( CHAIN C AND RESID 17:24 )C17 - 24
14X-RAY DIFFRACTION14( CHAIN C AND RESID 25:70 )C25 - 70
15X-RAY DIFFRACTION15( CHAIN C AND RESID 71:81 )C71 - 81
16X-RAY DIFFRACTION16( CHAIN C AND RESID 82:115 )C82 - 115
17X-RAY DIFFRACTION17( CHAIN C AND RESID 116:141 )C116 - 141
18X-RAY DIFFRACTION18( CHAIN C AND RESID 142:177 )C142 - 177
19X-RAY DIFFRACTION19( CHAIN D AND RESID 14:19 )D14 - 19
20X-RAY DIFFRACTION20( CHAIN D AND RESID 20:67 )D20 - 67
21X-RAY DIFFRACTION21( CHAIN D AND RESID 68:86 )D68 - 86
22X-RAY DIFFRACTION22( CHAIN D AND RESID 87:109 )D87 - 109
23X-RAY DIFFRACTION23( CHAIN D AND RESID 110:143 )D110 - 143
24X-RAY DIFFRACTION24( CHAIN D AND RESID 144:177 )D144 - 177

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