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

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Basic information

Entry
Database: PDB / ID: 4ylg
TitleStructure of an ADP ribosylation factor from Entamoeba histolytica HM-1:IMSS bound to Mg-GDP
ComponentsADP-ribosylation factorADP ribosylation factor
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 HM-1:IMSS (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsSeattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
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
DepositionMar 5, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.symmetry_operation / _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
B: ADP-ribosylation factor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5096
Polymers39,5742
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-329-

HOH

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Components

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


Mass: 19786.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Entamoeba histolytica HM-1:IMSS (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
PH range: 7

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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
RadiationMonochromator: Asymmetric cut single crystal Si(220) / Protocol: 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 / Redundancy: 4.12 % / 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
NameClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1R8S

1r8s


Resolution: 1.8→19.729 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1702 5 %Random selection
Rwork0.2228 32359 --
obs0.2254 34061 93.44 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.81 Å2 / Biso mean: 25.5245 Å2 / Biso min: 6.59 Å2
Refinement stepCycle: final / Resolution: 1.8→19.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2492 0 58 313 2863
Biso mean--16.08 33.46 -
Num. residues----326
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072649
X-RAY DIFFRACTIONf_angle_d1.143619
X-RAY DIFFRACTIONf_chiral_restr0.052430
X-RAY DIFFRACTIONf_plane_restr0.004445
X-RAY DIFFRACTIONf_dihedral_angle_d14.306967
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.85280.30251340.2322801X-RAY DIFFRACTION97
1.8528-1.91260.47531150.37382337X-RAY DIFFRACTION82
1.9126-1.98090.48611330.41942414X-RAY DIFFRACTION85
1.9809-2.06010.33631320.26992681X-RAY DIFFRACTION93
2.0601-2.15380.38351350.31962629X-RAY DIFFRACTION91
2.1538-2.26720.451110.33422571X-RAY DIFFRACTION88
2.2672-2.4090.30751490.24172676X-RAY DIFFRACTION93
2.409-2.59460.27621330.19962862X-RAY DIFFRACTION99
2.5946-2.8550.25221590.20222779X-RAY DIFFRACTION97
2.855-3.26650.20751630.18412871X-RAY DIFFRACTION99
3.2665-4.10940.20741560.16652779X-RAY DIFFRACTION96
4.1094-19.72990.19261820.15822959X-RAY DIFFRACTION99
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)
10.18320.03570.03891.0038-0.21170.0589-0.01360.02570.0454-0.15720.0246-0.04-0.4022-0.1021-0.03980.5105-0.08630.09350.5719-0.0964-0.038362.853211.36464.1695
22.4259-0.4976-0.05712.19810.8052.66640.02870.29850.0918-0.0840.21470.01170.04860.2119-0.1160.1773-0.0641-0.01360.13560.03670.038853.234512.871618.5963
33.47710.5379-0.62385.203-0.70673.9631-0.08410.0538-0.2416-0.11690.05220.07640.2591-0.07080.03180.1162-0.02280.00240.18950.02820.072946.61384.645216.5346
40.8418-0.0923-1.83061.99010.59294.16860.08570.64180.1338-0.11150.07230.1768-0.0193-0.1525-0.12020.1288-0.02220.01590.28080.02880.045352.95156.173715.1046
53.27351.15830.60175.7017-1.32630.5584-0.36620.3858-1.23730.1636-0.32560.07421.2699-0.42760.58040.5313-0.03440.01530.2266-0.05030.352358.3230.757723.9914
64.8875-2.5814-1.93424.67861.81414.8212-0.1470.0674-0.0940.27930.0919-0.00530.06260.02140.07690.1163-0.0242-0.0280.04850.01850.020958.615415.576124.2041
72.5974-1.4697-1.15954.3073.29944.3145-0.1646-0.0479-0.27380.37880.2631-0.17710.27730.0953-0.10090.259-0.0381-0.06220.15850.01860.05560.681813.079333.3352
85.5418-1.6823-0.96914.45391.24815.0775-0.07720.174-0.55520.1998-0.011-0.27150.47450.580.05380.1496-0.0033-0.01050.1743-0.02620.132165.676610.009921.6171
93.0058-2.70232.09323.7047-1.50242.4456-0.3489-0.17590.80030.10830.1739-0.3373-0.51650.01860.15980.2179-0.0206-0.03860.09360.01010.227358.829327.089129.3006
102.45731.0131-0.83651.83451.13193.1989-0.03320.24410.1731-0.21880.1529-0.3886-0.29650.3928-0.08640.1591-0.07230.03040.1201-0.00930.147464.998219.62422.2056
117.0495-1.6104-0.49183.80910.04833.35190.27570.91050.4535-0.8728-0.0461-0.429-0.30520.4299-0.17340.3049-0.09750.09770.3151-0.0060.133465.17518.254112.3359
122.25830.09650.04193.1951-0.2582.6858-0.08090.5339-0.2332-0.27330.00070.29650.0635-0.18120.00580.1347-0.0369-0.01480.2108-0.05920.141532.98365.153216.3391
132.4348-0.20760.04232.88780.22192.79670.00310.20980.00310.0087-0.02120.2933-0.1307-0.12240.03830.1226-0.02050.02170.05380.00320.162224.04315.119728.2981
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 13 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 33 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 34 through 46 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 63 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 64 through 80 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 81 through 92 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 93 through 108 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 109 through 122 )A0
9X-RAY DIFFRACTION9chain 'A' and (resid 123 through 138 )A0
10X-RAY DIFFRACTION10chain 'A' and (resid 139 through 161 )A0
11X-RAY DIFFRACTION11chain 'A' and (resid 162 through 173 )A0
12X-RAY DIFFRACTION12chain 'B' and (resid 3 through 64 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 65 through 173 )B0

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