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- PDB-4y0v: Structure of an ADP ribosylation factor from Entamoeba histolytic... -

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Basic information

Entry
Database: PDB / ID: 4y0v
TitleStructure of an ADP ribosylation factor from Entamoeba histolytica HM-1:IMSS bound to Mg-GDP
ComponentsADP-ribosylation factor 1ARF1
KeywordsSIGNALING PROTEIN / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID
Function / homology
Function and homology information


vesicle-mediated transport / intracellular protein transport / GTPase activity / GTP binding / Golgi apparatus / plasma membrane
Similarity search - Function
Small GTPase superfamily, ARF type / ADP-ribosylation factor 1-5 / 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 / small GTPase Rab1 family profile. / Rab subfamily of small GTPases / Small GTP-binding protein domain ...Small GTPase superfamily, ARF type / ADP-ribosylation factor 1-5 / 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 / small GTPase Rab1 family profile. / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / ADP-ribosylation factor
Similarity search - Component
Biological speciesEntamoeba histolytica (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease (SSGCID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200025C United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of an ADP-ribosylation factor, ARF1, from Entamoeba histolytica bound to Mg(2+)-GDP.
Authors: Serbzhinskiy, D.A. / Clifton, M.C. / Sankaran, B. / Staker, B.L. / Edwards, T.E. / Myler, P.J.
History
DepositionFeb 6, 2015Deposition site: RCSB / Processing site: RCSB
SupersessionMar 4, 2015ID: 3RD1
Revision 1.0Mar 4, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3May 20, 2015Group: Database references
Revision 1.4Sep 6, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.5Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.6Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.7Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 1
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3646
Polymers40,4292
Non-polymers9354
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3000 Å2
ΔGint-47 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.540, 40.660, 78.950
Angle α, β, γ (deg.)90.000, 97.450, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-328-

HOH

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Components

#1: Protein ADP-ribosylation factor 1 / ARF1 / ADP-ribosylation factor / putative / Small GTPase ArfA1


Mass: 20214.258 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica (eukaryote) / Gene: EHI_073470, EHI_137720 / Production host: Escherichia coli (E. coli) / References: UniProt: C4LXL1
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 313 / 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: 2.51 Å3/Da / Density % sol: 50.96 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 15% ethanol, 0.1M Tris, Cryoprotection 25% Ethylene glycol, pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→19.729 Å / Num. obs: 34091 / % possible obs: 93.4 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 15.96 Å2 / Rmerge F obs: 0.091 / Rmerge(I) obs: 0.06 / Rrim(I) all: 0.069 / Χ2: 0.973 / Net I/σ(I): 15.97 / Num. measured all: 141065
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.850.4050.4313.2411831268426000.48696.9
1.85-1.90.4930.4513.9110019258424000.51792.9
1.9-1.950.2110.1549.265711253517460.18568.9
1.95-2.010.2570.2366.0210554249024520.26998.5
2.01-2.080.1750.159.588007237921110.17788.7
2.08-2.150.1950.1848.559275230821550.2193.4
2.15-2.230.1450.13810.138730223320470.15891.7
2.23-2.320.1160.08614.46211216418210.10584.1
2.32-2.430.0760.0914.489189206520320.10198.4
2.43-2.550.0650.07416.668768199019660.08498.8
2.55-2.680.0710.07417.937552186818150.08597.2
2.68-2.850.0590.06319.977590178317480.07298
2.85-3.040.0390.04723.327250166816580.05499.4
3.04-3.290.030.04127.266763159015760.04699.1
3.29-3.60.0330.0429.555391144614030.04797
3.6-4.020.0310.04132.364358131012210.04793.2
4.02-4.650.0220.03134.664720116811600.03699.3
4.65-5.690.020.02835.43416710009970.03299.7
5.69-8.050.0170.02734.633347777770.03100
8.050.0140.02238.0516454514060.02690

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 54.57 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å19.73 Å
Translation2.5 Å19.73 Å

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: dev_1932)refinement
XDSdata scaling
XSCALE2.1.4data scaling
PHASERphasing
Cootmodel building
PDB_EXTRACTdata extraction
REFMAC5.5.0109refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1R8S

1r8s


Resolution: 1.8→19.729 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1702 5 %RANDOM
Rwork0.2226 32359 --
obs0.2252 34061 93.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.71 Å2 / Biso mean: 25.5495 Å2 / Biso min: 6.5 Å2
Refinement stepCycle: final / Resolution: 1.8→19.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 58 313 2863
Biso mean--16.17 33.43 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072649
X-RAY DIFFRACTIONf_angle_d1.1273619
X-RAY DIFFRACTIONf_chiral_restr0.052430
X-RAY DIFFRACTIONf_plane_restr0.004445
X-RAY DIFFRACTIONf_dihedral_angle_d14.374967
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85280.30021340.23032801293597
1.8528-1.91260.4771150.37392337245282
1.9126-1.98090.48731330.41962414254785
1.9809-2.06010.33741320.27062681281393
2.0601-2.15380.38081350.31842629276491
2.1538-2.26720.45251110.33382571268288
2.2672-2.4090.30821490.2422676282593
2.409-2.59460.27661330.19892862299599
2.5946-2.8550.25281590.20132779293897
2.855-3.26650.20861630.18392871303499
3.2665-4.10940.20611560.16632779293596
4.1094-19.72990.19281820.15872959314199
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)
10.09450.06270.0071.0199-0.23490.0614-0.03360.0610.0298-0.13840.0438-0.0322-0.4135-0.1455-0.05030.5081-0.09070.08810.5899-0.0963-0.002562.85311.3654.169
22.4028-0.4865-0.04462.18420.80112.66280.02560.30370.0969-0.10170.2240.00270.05140.2232-0.110.1765-0.0634-0.01370.13370.03680.040753.23412.8718.597
33.52280.489-0.57755.134-0.65313.8989-0.0990.0569-0.2422-0.13040.05370.0780.2631-0.05650.02750.1132-0.0258-0.00420.18810.03010.070446.6164.64516.535
40.8498-0.1017-1.80281.95790.60154.01930.09410.65720.1419-0.1050.07080.1896-0.0302-0.1488-0.11470.1346-0.02070.01450.2740.0310.046352.9516.17515.106
53.1541.20240.58565.6376-1.31060.5631-0.36240.3921-1.24320.1348-0.34120.0551.25-0.40970.55990.5389-0.04080.01430.2278-0.05760.357158.3230.75823.99
64.7786-2.5011-1.88544.54991.76124.8149-0.15730.0568-0.09360.28290.1036-0.03250.06220.03750.07890.1106-0.022-0.02880.04540.01750.023558.61615.57624.205
72.5285-1.3077-1.1314.14583.29214.2919-0.1552-0.0235-0.26790.34530.2497-0.19160.2550.0983-0.11030.2513-0.0325-0.05850.15830.01770.062760.67813.07933.339
85.5121-1.643-0.94714.35781.24385.0818-0.09310.166-0.57290.227-0.0169-0.25670.47930.57750.05060.1466-0.0012-0.00870.1754-0.02570.13465.67610.00721.618
93.0078-2.68042.06813.5914-1.47062.3764-0.3468-0.18020.7750.10030.1872-0.3177-0.51280.0090.16390.2212-0.0203-0.0360.10020.01210.224858.82927.0929.301
102.4781.0334-0.84991.83651.14523.2018-0.04560.24740.1697-0.22020.1613-0.3866-0.29250.3852-0.08730.1563-0.07320.0280.1304-0.01120.137264.99819.62422.206
116.9748-1.4669-0.54453.4961-0.09783.15420.29920.89440.4584-0.8559-0.0551-0.4262-0.28920.4099-0.15870.2907-0.08590.08820.3121-0.00240.137265.17718.25312.334
122.340.08630.0133.1874-0.2562.7355-0.08050.5424-0.2268-0.26750.00180.29520.0595-0.18640.00630.1356-0.0351-0.01840.2109-0.05970.141932.9845.15316.339
132.4269-0.19220.0232.88420.25312.83410.00140.2141-0.00580.0127-0.01860.2971-0.1408-0.1310.03730.1191-0.02110.02190.05040.00320.161624.0435.1228.298
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:13 )A3 - 13
2X-RAY DIFFRACTION2( CHAIN A AND RESID 14:33 )A14 - 33
3X-RAY DIFFRACTION3( CHAIN A AND RESID 34:46 )A34 - 46
4X-RAY DIFFRACTION4( CHAIN A AND RESID 47:63 )A47 - 63
5X-RAY DIFFRACTION5( CHAIN A AND RESID 64:80 )A64 - 80
6X-RAY DIFFRACTION6( CHAIN A AND RESID 81:92 )A81 - 92
7X-RAY DIFFRACTION7( CHAIN A AND RESID 93:108 )A93 - 108
8X-RAY DIFFRACTION8( CHAIN A AND RESID 109:122 )A109 - 122
9X-RAY DIFFRACTION9( CHAIN A AND RESID 123:138 )A123 - 138
10X-RAY DIFFRACTION10( CHAIN A AND RESID 139:161 )A139 - 161
11X-RAY DIFFRACTION11( CHAIN A AND RESID 162:173 )A162 - 173
12X-RAY DIFFRACTION12( CHAIN B AND RESID 3:64 )B3 - 64
13X-RAY DIFFRACTION13( CHAIN B AND RESID 65:173 )B65 - 173

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