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- PDB-2fe5: The Crystal Structure of the Second PDZ Domain of Human DLG3 -

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Basic information

Entry
Database: PDB / ID: 2fe5
TitleThe Crystal Structure of the Second PDZ Domain of Human DLG3
ComponentsPresynaptic protein SAP102Synapse
KeywordsSTRUCTURAL PROTEIN / PDZ domain / DLG3 / Human / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


establishment of planar polarity / NrCAM interactions / receptor localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission ...establishment of planar polarity / NrCAM interactions / receptor localization to synapse / Synaptic adhesion-like molecules / establishment or maintenance of epithelial cell apical/basal polarity / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / Activation of Ca-permeable Kainate Receptor / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / regulation of postsynaptic membrane neurotransmitter receptor levels / AMPA glutamate receptor complex / Long-term potentiation / bicellular tight junction / phosphatase binding / positive regulation of protein tyrosine kinase activity / Ras activation upon Ca2+ influx through NMDA receptor / postsynaptic density membrane / adherens junction / neuromuscular junction / cell-cell adhesion / kinase binding / chemical synaptic transmission / RAF/MAP kinase cascade / basolateral plasma membrane / neuron projection / negative regulation of cell population proliferation / glutamatergic synapse / ubiquitin protein ligase binding / extracellular space / plasma membrane / cytosol
Similarity search - Function
Disks Large homologue 3, SH3 domain / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain ...Disks Large homologue 3, SH3 domain / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / 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 / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.1 Å
AuthorsUgochukwu, E. / Phillips, C. / Schoch, G. / Berridge, G. / Salah, E. / Colebrook, S. / Smee, C. / Savitsky, P. / Bray, J. / Elkins, J. ...Ugochukwu, E. / Phillips, C. / Schoch, G. / Berridge, G. / Salah, E. / Colebrook, S. / Smee, C. / Savitsky, P. / Bray, J. / Elkins, J. / Doyle, D. / Bunkoczi, G. / Debreczeni, J. / Turnbull, A. / Gorrec, F. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: The Crystal Structure of the Second PDZ Domain of Human DLG3
Authors: Ugochukwu, E. / Phillips, C. / Schoch, G. / Berridge, G. / Salah, E. / Colebrook, S. / Smee, C. / Savitsky, P. / Bray, J. / Elkins, J. / Doyle, D. / Bunkoczi, G. / Debreczeni, J. / Turnbull, ...Authors: Ugochukwu, E. / Phillips, C. / Schoch, G. / Berridge, G. / Salah, E. / Colebrook, S. / Smee, C. / Savitsky, P. / Bray, J. / Elkins, J. / Doyle, D. / Bunkoczi, G. / Debreczeni, J. / Turnbull, A. / Gorrec, F. / von Delft, F. / Sundstrom, M. / Arrowsmith, C. / Weigelt, J. / Edwards, A. / Structural Genomics Consortium (SGC)
History
DepositionDec 15, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Presynaptic protein SAP102
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,1613
Polymers9,9721
Non-polymers1882
Water3,117173
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)26.487, 40.242, 33.340
Angle α, β, γ (deg.)90.00, 92.80, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Presynaptic protein SAP102 / Synapse / Synapse-associated protein 102 / Neuroendocrine-DLG / NE-DLG / Discs large homolog 3 / DLG3 / DLG3A


Mass: 9972.403 Da / Num. of mol.: 1 / Fragment: PDZ2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG3, KIAA1232 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q92796
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 173 / 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: 1.78 Å3/Da / Density % sol: 30.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: Ammonium sulphate, Glycerol, Bis-Tris, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9791 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 18, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.1→26.45 Å / Num. obs: 27971 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.1→1.16 Å / % possible all: 96.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2BYG.pdb

2byg


Resolution: 1.1→26.45 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.97 / SU B: 0.886 / SU ML: 0.02 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.032 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15038 1406 5 %RANDOM
Rwork0.11322 ---
all0.11512 26547 --
obs0.11512 26547 98.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 7.076 Å2
Baniso -1Baniso -2Baniso -3
1-0.23 Å20 Å20.15 Å2
2--0.1 Å20 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.1→26.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms698 0 11 173 882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022777
X-RAY DIFFRACTIONr_bond_other_d0.0010.02533
X-RAY DIFFRACTIONr_angle_refined_deg1.4391.9971050
X-RAY DIFFRACTIONr_angle_other_deg0.87331326
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3475104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64225.93832
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.615151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.292154
X-RAY DIFFRACTIONr_chiral_restr0.090.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02854
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02130
X-RAY DIFFRACTIONr_nbd_refined0.20.2144
X-RAY DIFFRACTIONr_nbd_other0.1820.2581
X-RAY DIFFRACTIONr_nbtor_refined0.1630.2355
X-RAY DIFFRACTIONr_nbtor_other0.0840.2416
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2122
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3040.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2780.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2330.248
X-RAY DIFFRACTIONr_mcbond_it3.2115645
X-RAY DIFFRACTIONr_mcbond_other1.8135207
X-RAY DIFFRACTIONr_mcangle_it3.6347794
X-RAY DIFFRACTIONr_scbond_it4.7519310
X-RAY DIFFRACTIONr_scangle_it6.05911252
X-RAY DIFFRACTIONr_rigid_bond_restr2.08731528
X-RAY DIFFRACTIONr_sphericity_free8.3693185
X-RAY DIFFRACTIONr_sphericity_bonded4.09131301
LS refinement shellResolution: 1.1→1.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 98 -
Rwork0.185 1894 -
obs--96.05 %

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