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- PDB-6x22: PDZ domain from choanoflagellate GIPC (mbGIPC) bound to GAIP peptide -

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Basic information

Entry
Database: PDB / ID: 6x22
TitlePDZ domain from choanoflagellate GIPC (mbGIPC) bound to GAIP peptide
ComponentsmbGIPC protein
KeywordsSIGNALING PROTEIN / PDZ / protein-protein interaction / peptide-binding domain / choanoflagellate / Monosiga brevicollis
Function / homology: / PDZ domain-containing protein GIPC1/2/3 / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PDZ domain-containing protein
Function and homology information
Biological speciesMonosiga brevicollis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.402 Å
AuthorsGao, M. / 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: mbGIPC protein


Theoretical massNumber of molelcules
Total (without water)10,2761
Polymers10,2761
Non-polymers00
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area5940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.729, 35.028, 82.548
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 mbGIPC protein


Mass: 10275.884 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 94-183)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Monosiga brevicollis (eukaryote) / Gene: 39217 / Plasmid: pET28a+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A9VCZ3
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / 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: 2.1 Å3/Da / Density % sol: 41.29 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 4% v/v Tacsimate, pH 4.0, 12% 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: Dec 13, 2019
RadiationMonochromator: Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 1.402→41.274 Å / Num. obs: 17577 / % possible obs: 96.8 % / Redundancy: 6.79 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 1 / Rsym value: 0.042 / Net I/σ(I): 22.08
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible all
1.402-1.496.521.6849370.6670.93593.5
1.49-1.596.93.2347790.8780.9696

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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 5V6B

5v6b


Resolution: 1.402→41.274 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2213 856 5.04 %
Rwork0.1867 16114 -
obs0.1885 16970 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 55.04 Å2 / Biso mean: 23.215 Å2 / Biso min: 12.91 Å2
Refinement stepCycle: final / Resolution: 1.402→41.274 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms697 0 0 124 821
Biso mean---31.16 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006734
X-RAY DIFFRACTIONf_angle_d0.867989
X-RAY DIFFRACTIONf_chiral_restr0.087113
X-RAY DIFFRACTIONf_plane_restr0.005130
X-RAY DIFFRACTIONf_dihedral_angle_d16.155283
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4022-1.49010.29971410.235255094
1.4901-1.60510.23131270.2012261896
1.6051-1.76660.22571270.1947264896
1.7666-2.02230.23021390.19266997
2.0223-2.54780.20861520.1967274498
2.5478-41.2740.21891700.1755288599

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