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- PDB-6x20: PDZ domain from choanoflagellate GIPC (mbGIPC) bound to B1AR peptide -

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Basic information

Entry
Database: PDB / ID: 6x20
TitlePDZ domain from choanoflagellate GIPC (mbGIPC) bound to B1AR peptide
ComponentsmbGIPC protein
KeywordsSIGNALING PROTEIN / PDZ / protein-protein interaction / peptide-binding domain / choanoflagellate / Monosiga brevicollis
Function / homology
Function and homology information


: / : / GIPC1-3 GH2 domain / GIPC1-3 GH1 domain / 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
Similarity search - Domain/homology
PDZ domain-containing protein
Similarity search - Component
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)10,3461
Polymers10,3461
Non-polymers00
Water1,838102
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 area6050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.787, 34.841, 81.604
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: 10346.040 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.: 102 / 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: 2.05 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate, pH 7.0, 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: 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→40.802 Å / Num. obs: 17334 / % possible obs: 99.9 % / Redundancy: 6.69 % / Biso Wilson estimate: 26.9 Å2 / CC1/2: 1 / Rsym value: 0.039 / Net I/σ(I): 21.58
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible all
1.402-1.496.161.3451960.6321.28299.5
1.49-1.596.572.6728720.860.682100

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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→40.802 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2258 870 5.03 %
Rwork0.2081 16436 -
obs0.209 17306 99.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 56.2 Å2 / Biso mean: 26.664 Å2 / Biso min: 15.49 Å2
Refinement stepCycle: final / Resolution: 1.402→40.802 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms702 0 0 102 804
Biso mean---34.27 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005761
X-RAY DIFFRACTIONf_angle_d0.7291027
X-RAY DIFFRACTIONf_chiral_restr0.087116
X-RAY DIFFRACTIONf_plane_restr0.005136
X-RAY DIFFRACTIONf_dihedral_angle_d17.702299
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
1.4023-1.49020.3641420.30632680
1.4902-1.60520.3091480.25572674
1.6052-1.76680.30271430.2222728
1.7668-2.02240.27261320.20252716
2.0224-2.5480.20841410.22212760
2.548-40.8020.2041640.19172878

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