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- PDB-6x1n: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1... -

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Basic information

Entry
Database: PDB / ID: 6x1n
TitleCrystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ3 (mbDLG-3)
ComponentsmbDLG-3 protein
KeywordsSIGNALING PROTEIN / PDZ / Peptide-Binding Domain / Choanoflagellate / Signaling
Function / homology
Function and homology information


receptor localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / receptor clustering / cell-cell adhesion / cell junction / protein kinase binding / plasma membrane
Similarity search - Function
: / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain ...: / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3-like domain superfamily / SH3 domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMonosiga brevicollis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMackley, I. / Amacher, J.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1904711 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis.
Authors: Gao, M. / Mackley, I.G.P. / Mesbahi-Vasey, S. / Bamonte, H.A. / Struyvenberg, S.A. / Landolt, L. / Pederson, N.J. / Williams, L.I. / Bahl, C.D. / Brooks 3rd, L. / Amacher, J.F.
History
DepositionMay 19, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 25, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: mbDLG-3 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,3703
Polymers11,1861
Non-polymers1842
Water2,792155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area480 Å2
ΔGint-0 kcal/mol
Surface area6530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.384, 44.749, 28.613
Angle α, β, γ (deg.)90.000, 97.950, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-242-

TYR

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Components

#1: Protein mbDLG-3 protein


Mass: 11185.752 Da / Num. of mol.: 1 / Fragment: UNP residues 232-336
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 209 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9UT73
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.13 Å3/Da / Density % sol: 42.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.02 M zinc chloride, 20% w/v PEG3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 12, 2020
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.303→38.515 Å / Num. obs: 23422 / % possible obs: 96.5 % / Redundancy: 3.16 % / Biso Wilson estimate: 14.9 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.021 / Net I/σ(I): 34.04
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible allRmerge(I) obs
1.4-1.422.096.2561910.9670.13683.5
1.38-1.483.0611.2968290.98797.70.096

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Aimless0.7.4data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6QJF

6qjf


Resolution: 1.4→38.515 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1692 1126 4.88 %
Rwork0.1576 21944 -
obs0.1581 23070 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 42.09 Å2 / Biso mean: 14.9667 Å2 / Biso min: 5.07 Å2
Refinement stepCycle: final / Resolution: 1.4→38.515 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms784 0 12 165 961
Biso mean--19.72 24.59 -
Num. residues----105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005830
X-RAY DIFFRACTIONf_angle_d0.8391120
X-RAY DIFFRACTIONf_chiral_restr0.084122
X-RAY DIFFRACTIONf_plane_restr0.005147
X-RAY DIFFRACTIONf_dihedral_angle_d17.856308
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.303-1.36180.18831180.1778246689
1.3618-1.43360.20071650.1709273499
1.4336-1.52340.18471410.16192751100
1.5234-1.64110.1751220.15772790100
1.6411-1.80620.16431190.16012798100
1.8062-2.06760.18191620.1572783100
2.0676-2.60480.16181510.15882800100
2.6048-38.5150.15761480.15082822100

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