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- PDB-6b3y: Crystal structure of the PH-like domain from DENND3 -

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Basic information

Entry
Database: PDB / ID: 6b3y
TitleCrystal structure of the PH-like domain from DENND3
ComponentsDENN domain-containing protein 3
KeywordsTRANSPORT PROTEIN / autophagy / guanine nucleotide exchange factor / PH-like fold
Function / homology
Function and homology information


regulation of Rab protein signal transduction / RAB GEFs exchange GTP for GDP on RABs / endosome to lysosome transport / guanyl-nucleotide exchange factor activity / protein catabolic process / cytoplasmic vesicle
Similarity search - Function
: / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN / Domain always found downstream of DENN domain, found in a variety of signalling proteins / Tripartite DENN domain / Tripartite DENN domain profile. / WD40 repeat, conserved site ...: / cDENN domain / dDENN domain / DENN domain, C-terminal lobe / DENN (AEX-3) domain / Domain found in a variety of signalling proteins, always encircled by uDENN and dDENN / Domain always found downstream of DENN domain, found in a variety of signalling proteins / Tripartite DENN domain / Tripartite DENN domain profile. / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
DENN domain-containing protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.852 Å
AuthorsKozlov, G. / Xu, J. / Menade, M. / Beaugrand, M. / Pan, T. / McPherson, P.S. / Gehring, K.
CitationJournal: J. Biol. Chem. / Year: 2018
Title: A PH-like domain of the Rab12 guanine nucleotide exchange factor DENND3 binds actin and is required for autophagy.
Authors: Xu, J. / Kozlov, G. / McPherson, P.S. / Gehring, K.
History
DepositionSep 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 3, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DENN domain-containing protein 3
B: DENN domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)58,4842
Polymers58,4842
Non-polymers00
Water3,891216
1
A: DENN domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)29,2421
Polymers29,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DENN domain-containing protein 3


Theoretical massNumber of molelcules
Total (without water)29,2421
Polymers29,2421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.006, 82.006, 161.448
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein DENN domain-containing protein 3


Mass: 29241.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Dennd3, Kiaa0870 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A2RT67
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.24 M sodium malonate pH 7.0, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9768 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9768 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 46621 / % possible obs: 97.76 % / Redundancy: 7.8 % / Rsym value: 0.061 / Net I/σ(I): 37.2
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 4568 / Rsym value: 0.647 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.852→32.615 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.73
RfactorNum. reflection% reflection
Rfree0.2431 2340 5.02 %
Rwork0.1946 --
obs0.1969 46621 97.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.852→32.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 0 0 216 3827
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013680
X-RAY DIFFRACTIONf_angle_d1.1274962
X-RAY DIFFRACTIONf_dihedral_angle_d5.5592255
X-RAY DIFFRACTIONf_chiral_restr0.072566
X-RAY DIFFRACTIONf_plane_restr0.007625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8517-1.88950.33181240.26912565X-RAY DIFFRACTION98
1.8895-1.93060.26971490.24032554X-RAY DIFFRACTION98
1.9306-1.97550.25691310.21252606X-RAY DIFFRACTION99
1.9755-2.02490.25281340.19942601X-RAY DIFFRACTION99
2.0249-2.07960.2341370.1972611X-RAY DIFFRACTION99
2.0796-2.14080.2231370.18862591X-RAY DIFFRACTION99
2.1408-2.20990.22871570.18852603X-RAY DIFFRACTION99
2.2099-2.28890.20381360.18852589X-RAY DIFFRACTION99
2.2889-2.38050.25621420.1972588X-RAY DIFFRACTION98
2.3805-2.48880.27171320.20472618X-RAY DIFFRACTION98
2.4888-2.61990.27491470.20952588X-RAY DIFFRACTION98
2.6199-2.7840.26061660.21552569X-RAY DIFFRACTION98
2.784-2.99880.26961240.21112619X-RAY DIFFRACTION98
2.9988-3.30040.24411330.20742635X-RAY DIFFRACTION97
3.3004-3.77730.24151550.18752564X-RAY DIFFRACTION96
3.7773-4.75670.2077990.17052638X-RAY DIFFRACTION95
4.7567-32.620.24071370.19082742X-RAY DIFFRACTION94

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