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- PDB-6x1r: Crystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1... -

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Basic information

Entry
Database: PDB / ID: 6x1r
TitleCrystal Structure of Choanoflagellate (Monosiga brevicollis) Dlg1 PDZ2 (mbDLG-2) in spacegroup P212121
ComponentsmbDLG protein
KeywordsSIGNALING PROTEIN / PDZ / protein-protein interaction / choanoflagellates / Monosiga brevicollis / peptide-binding domain
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 / Pdz3 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 / Pdz3 Domain / 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 / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMonosiga brevicollis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsBamonte, H.A. / 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

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Assembly

Deposited unit
A: mbDLG protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9392
Polymers10,8471
Non-polymers921
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-0 kcal/mol
Surface area5340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.091, 56.107, 57.918
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein mbDLG protein


Mass: 10847.223 Da / Num. of mol.: 1 / Fragment: second PDZ domain (UNP residues 93-192)
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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.2 M sodium malonate, pH 5, 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: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.3→40.3 Å / Num. obs: 28809 / % possible obs: 99.4 % / Redundancy: 6.04 % / Biso Wilson estimate: 24.3 Å2 / CC1/2: 1 / Rsym value: 0.033 / Net I/σ(I): 24.04
Reflection shell

CC1/2: 0.866 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsRsym value% possible all
1.3-1.383.612.4884630.3696.5
1.38-1.4765.4282410.24399.9

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2BYG

2byg


Resolution: 1.3→40.299 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 21.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2072 1432 4.99 %
Rwork0.195 27248 -
obs0.1956 28680 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 75.48 Å2 / Biso mean: 24.4252 Å2 / Biso min: 11.85 Å2
Refinement stepCycle: final / Resolution: 1.3→40.299 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 0 6 123 826
Biso mean--44.96 33.14 -
Num. residues----94
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005732
X-RAY DIFFRACTIONf_angle_d0.769989
X-RAY DIFFRACTIONf_chiral_restr0.083112
X-RAY DIFFRACTIONf_plane_restr0.004132
X-RAY DIFFRACTIONf_dihedral_angle_d25.536271
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3003-1.34680.26191520.2667256496
1.3468-1.40070.2411380.22592681100
1.4007-1.46450.23851280.21452720100
1.4645-1.54170.24981420.21272699100
1.5417-1.63830.2411510.20672676100
1.6383-1.76480.21571290.20672741100
1.7648-1.94240.21431620.19972720100
1.9424-2.22340.2051500.17942742100
2.2234-2.80120.22791250.1992799100
2.8012-40.2990.18031550.18642906100

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