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- PDB-3dwd: Crystal structure of the ArfGAP domain of human ARFGAP1 -

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Basic information

Entry
Database: PDB / ID: 3dwd
TitleCrystal structure of the ArfGAP domain of human ARFGAP1
ComponentsADP-ribosylation factor GTPase-activating protein 1
KeywordsTRANSPORT PROTEIN / GAP / GTPASE ACTIVATING PROTEIN / STRUCTURAL GENOMICS CONSORTIUM (SGC) / ER-Golgi transport / Golgi apparatus / GTPase activation / Metal-binding / Phosphoprotein / Protein transport / Transport / Zinc-finger
Function / homology
Function and homology information


XBP1(S) activates chaperone genes / regulation of ARF protein signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / regulation of endocytosis / COPI-mediated anterograde transport / vesicle-mediated transport / GTPase activator activity / protein transport / Clathrin-mediated endocytosis / Golgi membrane ...XBP1(S) activates chaperone genes / regulation of ARF protein signal transduction / COPI-dependent Golgi-to-ER retrograde traffic / regulation of endocytosis / COPI-mediated anterograde transport / vesicle-mediated transport / GTPase activator activity / protein transport / Clathrin-mediated endocytosis / Golgi membrane / synapse / metal ion binding / cytosol
Similarity search - Function
Arf GTPase activating protein / Arf GTPase activating protein / ArfGAP domain superfamily / Putative GTPase activating protein for Arf / ARF GTPase-activating proteins domain profile. / Putative GTP-ase activating proteins for the small GTPase, ARF / ARFGAP/RecO-like zinc finger / Annexin V; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ADP-ribosylation factor GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the ArfGAP domain of human ARFGAP1
Authors: Nedyalkova, L. / Tong, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Wilkstrom, M. / Bochkarev, A. / Park, H.
History
DepositionJul 22, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Aug 30, 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 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)33,8316
Polymers33,7002
Non-polymers1314
Water19811
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)82.422, 82.422, 81.008
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
DetailsTHE AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS MACROMOLECULE IS UNKNOWN.

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Components

#1: Protein ADP-ribosylation factor GTPase-activating protein 1 / ADP-ribosylation factor 1 GTPase-activating protein / ARF1 GAP / ARF1-directed GTPase-activating ...ADP-ribosylation factor 1 GTPase-activating protein / ARF1 GAP / ARF1-directed GTPase-activating protein / GAP protein


Mass: 16850.082 Da / Num. of mol.: 2 / Fragment: Arf-GAP domain, UNP residues 1-128
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARFGAP1, ARF1GAP / Plasmid: pET28a-LIC (GI:145307000) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-V2R / References: UniProt: Q8N6T3
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 2 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.36 Å3/Da / Density % sol: 47.81 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 3.5M Sodium Formate, 0.1M Tris, 1:100 chymotrypsin, pH 8.5, vapor diffusion, sitting drop, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 12298 / % possible obs: 99.6 % / Redundancy: 7.4 % / Rmerge(I) obs: 0.092 / Χ2: 1.3 / Net I/σ(I): 8.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.4-2.446.50.6535910.91198.3
2.44-2.4970.66170.901199.5
2.49-2.537.20.5856130.9251100
2.53-2.597.50.5676240.921100
2.59-2.647.60.4416130.9721100
2.64-2.77.60.3676150.9791100
2.7-2.777.70.2946050.9571100
2.77-2.857.60.2796170.9951100
2.85-2.937.60.2096031.0261100
2.93-3.027.60.1776241.05199.8
3.02-3.137.50.1296101.091199.8
3.13-3.267.60.116191.141199.8
3.26-3.417.60.0926161.223199.8
3.41-3.587.50.0766181.255199.8
3.58-3.817.60.0596021.33199.8
3.81-4.17.60.0556271.62199.7
4.1-4.527.50.0636132.163199.5
4.52-5.177.50.0666172.546199.4
5.17-6.517.30.0576241.862199
6.51-507.30.0376302.06197.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.21 Å
Translation2.5 Å41.21 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.5.0044refinement
PDB_EXTRACT3.005data extraction
DMphasing
MolProbitymodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2gf9

2gf9


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.899 / WRfactor Rfree: 0.261 / WRfactor Rwork: 0.222 / SU B: 23.85 / SU ML: 0.244 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.273 588 4.794 %thin shells
Rwork0.234 ---
obs0.236 12266 99.537 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.648 Å2
Baniso -1Baniso -2Baniso -3
1--2.321 Å2-1.16 Å20 Å2
2---2.321 Å20 Å2
3---3.481 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1757 0 4 11 1772
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0211806
X-RAY DIFFRACTIONr_bond_other_d0.0010.021201
X-RAY DIFFRACTIONr_angle_refined_deg1.4451.9262445
X-RAY DIFFRACTIONr_angle_other_deg0.9243.0072886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2175226
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.52123.65982
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.08715272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7751511
X-RAY DIFFRACTIONr_chiral_restr0.0730.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022043
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02396
X-RAY DIFFRACTIONr_mcbond_it1.30921138
X-RAY DIFFRACTIONr_mcbond_other0.3242466
X-RAY DIFFRACTIONr_mcangle_it2.02531791
X-RAY DIFFRACTIONr_scbond_it1.5362668
X-RAY DIFFRACTIONr_scangle_it2.1813654
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4-2.46200.28188589998.443
2.462-2.5290.325720.27880087399.885
2.529-2.6020.418450.29181085799.767
2.602-2.68100.29383183299.88
2.681-2.7680.325620.26374280599.876
2.768-2.8650.289520.264721773100
2.865-2.9720.364490.259711760100
2.972-3.0920.296460.23766871599.86
3.092-3.22800.25970470599.858
3.228-3.3830.218300.23462665899.696
3.383-3.5640.242320.23360463899.687
3.564-3.7770.285340.2156459999.833
3.777-4.0330.228320.18953456799.824
4.033-4.3490.219440.18748553199.623
4.349-4.7550.216180.20746848899.59
4.755-5.2990.27180.22242644899.107
5.299-6.0870.275250.22636539498.985
6.087-7.380.349130.25132234198.24
7.38-10.1350.253100.21525327097.407
10.135-300.25860.2515917097.059
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)
16.28222.9208-1.3299.9794-1.883.76660.0166-0.2826-0.86690.7418-0.076-0.7078-0.2738-0.22810.05940.08070.0244-0.03840.04420.03030.198430.6908-9.39060.1581
24.7281.60510.58777.99021.85582.9756-0.0068-0.00350.876-0.3478-0.08110.3805-0.3787-0.29220.08790.15360.03790.00870.1217-0.01890.230930.0409-12.3032-38.317
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 120
2X-RAY DIFFRACTION2B3 - 120

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