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- PDB-7yir: Crystal structure of N-terminal PH domain of ARAP3 protein from human -

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Basic information

Entry
Database: PDB / ID: 7yir
TitleCrystal structure of N-terminal PH domain of ARAP3 protein from human
ComponentsArf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
KeywordsCYTOSOLIC PROTEIN / ARAP3 / PH domain
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 / ruffle / cytoskeleton organization / 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 / ruffle / cytoskeleton organization / RAC1 GTPase cycle / lamellipodium / cytoskeleton / signal transduction / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
ARAP, RhoGAP domain / 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 ...ARAP, RhoGAP domain / 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
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / 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: 2.099 Å
AuthorsZhang, Y.J. / Liu, Y.R. / Wu, B.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2023
Title: Structural Insights Uncover the Specific Phosphoinositide Recognition by the PH1 Domain of Arap3.
Authors: Zhang, Y. / Ge, L. / Xu, L. / Liu, Y. / Wang, J. / Liu, C. / Zhao, H. / Xing, L. / Wang, J. / Wu, B.
History
DepositionJul 18, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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: Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,1632
Polymers13,0571
Non-polymers1061
Water64936
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint2 kcal/mol
Surface area6130 Å2
Unit cell
Length a, b, c (Å)102.634, 102.634, 45.506
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-318-

HOH

21A-331-

HOH

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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: 13056.944 Da / Num. of mol.: 1 / Fragment: PH1 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARAP3, CENTD3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8WWN8
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 36 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS (pH 6.5), 30% v/v Polyethylene glycol monomethyl ether 550

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 2.099→50 Å / Num. obs: 8653 / % possible obs: 99.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.113 / Net I/σ(I): 20.5
Reflection shellResolution: 2.099→2.14 Å / Rmerge(I) obs: 0.357 / Num. unique obs: 429

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Processing

Software
NameVersionClassification
SCALAdata scaling
PHENIX1.19.2-4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UPR

1upr


Resolution: 2.099→33.595 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.23 424 5.2 %
Rwork0.1845 7726 -
obs0.1867 8150 93.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.69 Å2 / Biso mean: 37.2688 Å2 / Biso min: 16.98 Å2
Refinement stepCycle: final / Resolution: 2.099→33.595 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms799 0 17 36 852
Biso mean--42.18 34.61 -
Num. residues----99
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009822
X-RAY DIFFRACTIONf_angle_d0.9761103
X-RAY DIFFRACTIONf_chiral_restr0.053118
X-RAY DIFFRACTIONf_plane_restr0.007142
X-RAY DIFFRACTIONf_dihedral_angle_d16.679499
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0992-2.40290.24861450.1811243291
2.4029-3.02710.26831430.198253394
3.0271-33.5950.20321360.1794276196
Refinement TLS params.Method: refined / Origin x: 27.4534 Å / Origin y: -29.2362 Å / Origin z: 0.9186 Å
111213212223313233
T0.2011 Å2-0.0183 Å20.0014 Å2-0.126 Å20.0126 Å2--0.1668 Å2
L4.4891 °20.1628 °20.0976 °2-1.8161 °20.0968 °2--3.6084 °2
S-0.1353 Å °-0.058 Å °0.0359 Å °0.0923 Å °0.0382 Å °0.1347 Å °-0.1148 Å °-0.0447 Å °0.0893 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 3 through 101)

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