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- PDB-1o3y: Crystal structure of mouse ARF1 (delta17-Q71L), GTP form -

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Basic information

Entry
Database: PDB / ID: 1o3y
TitleCrystal structure of mouse ARF1 (delta17-Q71L), GTP form
ComponentsADP-ribosylation factor 1ARF1
KeywordsPROTEIN TRANSPORT
Function / homology
Function and homology information


synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / mitotic cleavage furrow ingression ...synaptic vesicle budding / lysosomal membrane organization / positive regulation of late endosome to lysosome transport / regulation of phospholipid metabolic process / Golgi to transport vesicle transport / trans-Golgi Network Vesicle Budding / phospholipase D activator activity / Synthesis of PIPs at the Golgi membrane / Intra-Golgi traffic / mitotic cleavage furrow ingression / positive regulation of ER to Golgi vesicle-mediated transport / Lysosome Vesicle Biogenesis / COPI-mediated anterograde transport / regulation of receptor internalization / very-low-density lipoprotein particle assembly / regulation of Arp2/3 complex-mediated actin nucleation / Synthesis of PIPs at the plasma membrane / COPI-dependent Golgi-to-ER retrograde traffic / positive regulation of calcium ion-dependent exocytosis / postsynaptic actin cytoskeleton organization / Golgi Associated Vesicle Biogenesis / MHC class II antigen presentation / dendritic spine organization / long-term synaptic depression / positive regulation of dendritic spine development / positive regulation of sodium ion transmembrane transport / positive regulation of endocytosis / cell leading edge / intracellular copper ion homeostasis / endomembrane system / vesicle-mediated transport / sarcomere / small monomeric GTPase / actin filament organization / positive regulation of protein secretion / intracellular protein transport / cellular response to virus / GDP binding / protein transport / late endosome / postsynaptic density / neuron projection / protein domain specific binding / Golgi membrane / GTPase activity / glutamatergic synapse / GTP binding / Golgi apparatus / magnesium ion binding / protein-containing complex / plasma membrane / cytosol
Similarity search - Function
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 / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase ...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 / 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'-TRIPHOSPHATE / ADP-ribosylation factor 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsShiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
CitationJournal: Nat.Struct.Biol. / Year: 2003
Title: Molecular mechanism of membrane recruitment of GGA by ARF in lysosomal protein transport
Authors: Shiba, T. / Kawasaki, M. / Takatsu, H. / Nogi, T. / Matsugaki, N. / Igarashi, N. / Suzuki, M. / Kato, R. / Nakayama, K. / Wakatsuki, S.
History
DepositionMay 8, 2003Deposition site: RCSB / Processing site: PDBJ
SupersessionMay 20, 2003ID: 1J2I
Revision 1.0May 20, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_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 / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)38,9986
Polymers37,9032
Non-polymers1,0954
Water5,639313
1
A: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4993
Polymers18,9521
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ADP-ribosylation factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4993
Polymers18,9521
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)127.605, 50.770, 52.081
Angle α, β, γ (deg.)90.00, 113.37, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein ADP-ribosylation factor 1 / ARF1 / ARF1


Mass: 18951.615 Da / Num. of mol.: 2 / Fragment: RESIDUES 18-181 / Mutation: Q71L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pProEX HT / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P84078
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#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: 1.82 Å3/Da / Density % sol: 31.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: PEG3350, ammonium acetate, acetate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.977 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 14, 2002
RadiationMonochromator: SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.977 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 44086 / Num. obs: 44072 / % possible obs: 89.8 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 12.9
Reflection shellResolution: 1.5→1.58 Å / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3.1 / % possible all: 62.8

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SOLVEphasing
RESOLVEmodel building
REFMAC5refinement
CCP4(SCALA)data scaling
RESOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HFV

1hfv
PDB Unreleased entry


Resolution: 1.5→20 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.932 / SU B: 1.546 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.093 / ESU R Free: 0.087 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.21084 2221 5 %RANDOM
Rwork0.18998 ---
all0.19104 44072 --
obs0.19104 41851 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.332 Å2
Baniso -1Baniso -2Baniso -3
1-0.24 Å20 Å20.19 Å2
2--0.12 Å20 Å2
3----0.2 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2664 0 66 313 3043
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212778
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3841.9783774
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.0513330
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.34815493
X-RAY DIFFRACTIONr_chiral_restr0.0910.2422
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022064
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2480.31295
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.5280
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2170.391
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.8630.537
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.7071.51642
X-RAY DIFFRACTIONr_mcangle_it1.3122640
X-RAY DIFFRACTIONr_scbond_it2.09631136
X-RAY DIFFRACTIONr_scangle_it3.2934.51134
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.269 81
Rwork0.239 1910

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