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- PDB-5jd0: crystal structure of ARAP3 RhoGAP domain -

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Basic information

Entry
Database: PDB / ID: 5jd0
Titlecrystal structure of ARAP3 RhoGAP domain
ComponentsArf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
KeywordsSIGNALING PROTEIN / ARAP3 / RhoGAP
Function / homology
Function and homology information


phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / cytoskeleton organization / ruffle / RAC1 GTPase cycle / lamellipodium ...phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,4,5-trisphosphate binding / CDC42 GTPase cycle / RHOA GTPase cycle / RAC3 GTPase cycle / vesicle-mediated transport / cytoskeleton organization / ruffle / RAC1 GTPase cycle / lamellipodium / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
ARAP, RhoGAP domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation 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 / Ras-associating (RA) domain profile. ...ARAP, RhoGAP domain / Phosphatidylinositol 3-kinase; Chain A / Rho GTPase activation 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 / Ras-associating (RA) domain profile. / Ras association (RalGDS/AF-6) domain / Ras-associating (RA) domain / Rho GTPase-activating protein domain / RhoGAP domain / Rho GTPase-activating proteins domain profile. / GTPase-activator protein for Rho-like GTPases / Rho GTPase activation protein / SAM domain (Sterile alpha motif) / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / PH domain / Sterile alpha motif/pointed domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily / Ubiquitin-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBao, H. / Li, F. / Wu, J. / Shi, Y.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for the Specific Recognition of RhoA by the Dual GTPase-activating Protein ARAP3
Authors: Bao, H. / Li, F. / Wang, C. / Wang, N. / Jiang, Y. / Tang, Y. / Wu, J. / Shi, Y.
History
DepositionApr 15, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2016Group: Database references
Revision 1.2Nov 8, 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)48,3722
Polymers48,3722
Non-polymers00
Water1,60389
1
A: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)24,1861
Polymers24,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)24,1861
Polymers24,1861
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.510, 108.510, 95.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3 / Centaurin-delta-3 / Cnt-d3


Mass: 24185.779 Da / Num. of mol.: 2 / Fragment: UNP residues 906-1107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: Q8WWN8
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 3.04 Å3/Da / Density % sol: 59.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 / Details: 100 mM HEPES, 10% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97931 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 23, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 2.3→76.728 Å / Num. all: 25608 / Num. obs: 25608 / % possible obs: 99.1 % / Redundancy: 9.1 % / Biso Wilson estimate: 36.17 Å2 / Rpim(I) all: 0.049 / Rrim(I) all: 0.147 / Rsym value: 0.138 / Net I/av σ(I): 3.304 / Net I/σ(I): 11.1 / Num. measured all: 232624
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.3-2.429.40.6421.23452236840.2190.6790.6423.8100
2.42-2.579.40.4061.93296635240.1390.4290.4065.6100
2.57-2.759.30.282.73065232850.0960.2960.287.5100
2.75-2.979.30.1993.62876130990.0680.2110.1999.7100
2.97-3.259.30.1424.82634228450.0490.1510.14212.8100
3.25-3.6490.1175.22333925820.0410.1240.11715.599.2
3.64-4.28.50.1363.81794421160.050.1450.1361791.8
4.2-5.148.70.1095.31731619850.0390.1160.10918.8100
5.14-7.278.50.0876.31329515670.0310.0930.08718.2100
7.27-38.3648.10.0776.774879210.0290.0830.07719.798.6

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
SCALA3.3.22data scaling
PDB_EXTRACT3.2data extraction
SCALAdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EE5

2ee5


Resolution: 2.3→38.364 Å / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 1301 5.09 %
Rwork0.2202 --
obs0.2222 25555 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→38.364 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3088 0 0 89 3177
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083135
X-RAY DIFFRACTIONf_angle_d0.9164250
X-RAY DIFFRACTIONf_dihedral_angle_d18.2631906
X-RAY DIFFRACTIONf_chiral_restr0.052500
X-RAY DIFFRACTIONf_plane_restr0.006555
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.39210.3431150.2492685X-RAY DIFFRACTION100
2.3921-2.5010.29511480.23182671X-RAY DIFFRACTION100
2.501-2.63280.28591570.22292665X-RAY DIFFRACTION100
2.6328-2.79770.27091410.21782679X-RAY DIFFRACTION100
2.7977-3.01370.30391550.2452685X-RAY DIFFRACTION100
3.0137-3.31680.27771380.24212704X-RAY DIFFRACTION100
3.3168-3.79640.27171330.23352518X-RAY DIFFRACTION92
3.7964-4.78160.23841470.19182761X-RAY DIFFRACTION100
4.7816-38.36940.21871670.21022886X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -9.8014 Å / Origin y: -39.1162 Å / Origin z: 11.9869 Å
111213212223313233
T0.2057 Å20.0438 Å2-0.0466 Å2-0.1564 Å2-0.0209 Å2--0.2862 Å2
L2.0313 °20.4299 °2-0.5279 °2-0.975 °20.4514 °2--1.3472 °2
S-0.084 Å °-0.0079 Å °-0.0635 Å °0.0467 Å °0.0682 Å °-0.0497 Å °0.08 Å °-0.002 Å °0.0257 Å °
Refinement TLS groupSelection details: all

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