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- PDB-2he2: Crystal structure of the 3rd PDZ domain of human discs large homo... -

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Basic information

Entry
Database: PDB / ID: 2he2
TitleCrystal structure of the 3rd PDZ domain of human discs large homologue 2, DLG2
ComponentsDiscs large homolog 2
KeywordsSIGNALING PROTEIN / DLG2 / PDZ / PDZ domain / signal transduction / Structural Genomics / Structural Genomics Consortium / SGC
Function / homology
Function and homology information


retrograde axonal protein transport / GMP kinase activity / anterograde axonal protein transport / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to potassium ion / juxtaparanode region of axon / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins ...retrograde axonal protein transport / GMP kinase activity / anterograde axonal protein transport / receptor localization to synapse / protein localization to synapse / establishment or maintenance of epithelial cell apical/basal polarity / cellular response to potassium ion / juxtaparanode region of axon / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / receptor clustering / Negative regulation of NMDA receptor-mediated neuronal transmission / Unblocking of NMDA receptors, glutamate binding and activation / Long-term potentiation / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / axon cytoplasm / Ras activation upon Ca2+ influx through NMDA receptor / adherens junction / postsynaptic density membrane / neuromuscular junction / cell-cell adhesion / kinase binding / nervous system development / RAF/MAP kinase cascade / basolateral plasma membrane / chemical synaptic transmission / perikaryon / neuron projection / postsynaptic density / protein kinase binding / membrane / plasma membrane / cytosol
Similarity search - Function
Disks Large homologue 2, SH3 domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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. ...Disks Large homologue 2, SH3 domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / 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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsTurnbull, A.P. / Phillips, C. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Papagrigoriou, E. / Debreczeni, J. / Gorrec, F. / Elkins, J.M. / von Delft, F. ...Turnbull, A.P. / Phillips, C. / Berridge, G. / Savitsky, P. / Smee, C.E.A. / Papagrigoriou, E. / Debreczeni, J. / Gorrec, F. / Elkins, J.M. / von Delft, F. / Weigelt, J. / Edwards, A. / Arrowsmith, C. / Sundstrom, M. / Doyle, D.A. / Structural Genomics Consortium (SGC)
CitationJournal: Protein Sci. / Year: 2007
Title: Structure of PICK1 and other PDZ domains obtained with the help of self-binding C-terminal extensions.
Authors: Elkins, J.M. / Papagrigoriou, E. / Berridge, G. / Yang, X. / Phillips, C. / Gileadi, C. / Savitsky, P. / Doyle, D.A.
History
DepositionJun 21, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Discs large homolog 2
B: Discs large homolog 2


Theoretical massNumber of molelcules
Total (without water)21,3542
Polymers21,3542
Non-polymers00
Water6,612367
1
A: Discs large homolog 2


Theoretical massNumber of molelcules
Total (without water)10,6771
Polymers10,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Discs large homolog 2


Theoretical massNumber of molelcules
Total (without water)10,6771
Polymers10,6771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.155, 56.070, 60.472
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Discs large homolog 2 / Postsynaptic density protein PSD-93 / Channel- associated protein of synapse-110 / Chapsyn-110


Mass: 10676.890 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DLG2 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3/Rosetta / References: UniProt: Q15700
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 367 / 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: 2.23 Å3/Da / Density % sol: 44.81 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 25.5% PEG 3350; 0.17M (NH4)2SO4; 15% glycerol , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.97646 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 6, 2006
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97646 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 30918 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.5→1.55 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Swissmodel based upon the coordinates of pdb entries 1TP5, 1TP3, 1BFE and 1BE9.

1tp5

1tp3

1bfe

1be9


Resolution: 1.5→41.13 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.477 / SU ML: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.077 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18688 1559 5.1 %RANDOM
Rwork0.12686 ---
all0.12987 29281 --
obs0.12987 29281 98.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.045 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.5→41.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1546 0 0 367 1913
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221572
X-RAY DIFFRACTIONr_bond_other_d0.0030.021056
X-RAY DIFFRACTIONr_angle_refined_deg1.3241.9632131
X-RAY DIFFRACTIONr_angle_other_deg0.85832594
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9215217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52224.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.16815263
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.536159
X-RAY DIFFRACTIONr_chiral_restr0.0790.2236
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021832
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02309
X-RAY DIFFRACTIONr_nbd_refined0.2020.2276
X-RAY DIFFRACTIONr_nbd_other0.1920.21177
X-RAY DIFFRACTIONr_nbtor_refined0.1690.2772
X-RAY DIFFRACTIONr_nbtor_other0.0830.2847
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.2226
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2640.222
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3770.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1980.249
X-RAY DIFFRACTIONr_mcbond_it4.03251058
X-RAY DIFFRACTIONr_mcbond_other2.5565440
X-RAY DIFFRACTIONr_mcangle_it4.51271625
X-RAY DIFFRACTIONr_scbond_it5.8449572
X-RAY DIFFRACTIONr_scangle_it7.25412499
X-RAY DIFFRACTIONr_rigid_bond_restr2.73832818
X-RAY DIFFRACTIONr_sphericity_free9.2393367
X-RAY DIFFRACTIONr_sphericity_bonded4.86832597
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 104 -
Rwork0.119 2033 -
obs--96.35 %

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