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- PDB-6x1x: PDZ domain from choanoflagellate GIPC (mbGIPC) -

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Basic information

Entry
Database: PDB / ID: 6x1x
TitlePDZ domain from choanoflagellate GIPC (mbGIPC)
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: 1.198 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

Downloads & links

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Assembly

Deposited unit
A: mbGIPC protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,4982
Polymers10,4061
Non-polymers921
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-0 kcal/mol
Surface area6180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)29.709, 35.301, 82.773
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: 10406.070 Da / Num. of mol.: 1 / Fragment: PDZ domain (UNP residues 94-187)
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: 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.: 189 / 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: 2.06 Å3/Da / Density % sol: 40.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M ammonium tartrate dibasic, pH 7.0, 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: May 10, 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: 1.198→41.386 Å / Num. obs: 28166 / % possible obs: 91.4 % / Redundancy: 5.34 % / Biso Wilson estimate: 12.3 Å2 / CC1/2: 1 / Rsym value: 0.914 / Net I/σ(I): 31.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rsym value% possible all
1.2-1.271.635.1545220.9730.11552.9
1.27-1.362.868.7576040.9870.09393.8

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Processing

Software
NameVersionClassification
Aimless0.7.1data 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: 1.198→41.386 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 18.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.189 1335 4.94 %
Rwork0.1666 25676 -
obs0.1678 27011 95.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 45.64 Å2 / Biso mean: 12.373 Å2 / Biso min: 3.91 Å2
Refinement stepCycle: final / Resolution: 1.198→41.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms707 0 6 189 902
Biso mean--18.14 21 -
Num. residues----93
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005779
X-RAY DIFFRACTIONf_angle_d0.8181053
X-RAY DIFFRACTIONf_chiral_restr0.086119
X-RAY DIFFRACTIONf_plane_restr0.005139
X-RAY DIFFRACTIONf_dihedral_angle_d15.313305
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.198-1.24060.2605910.2064179768
1.2406-1.29030.21721360.1821237891
1.2903-1.3490.20131280.1711262199
1.349-1.42010.18941180.16882646100
1.4201-1.50910.19791500.16512631100
1.5091-1.62560.19641310.15832665100
1.6256-1.78920.20021520.16732669100
1.7892-2.04810.17271480.16482672100
2.0481-2.58030.17541250.1642747100
2.5803-41.3860.18491560.16432850100

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