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- PDB-2wl7: Crystal structure of the PSD93 PDZ1 domain -

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Basic information

Entry
Database: PDB / ID: 2wl7
TitleCrystal structure of the PSD93 PDZ1 domain
ComponentsDISKS LARGE HOMOLOG 2
KeywordsTRANSFERASE / DELTA2 RECEPTOR INTERACTING PROTEIN / DLG2 / MAGUK / PSD93 / PDZ DOMAIN / CHAPSYN-110
Function / homology
Function and homology information


retrograde axonal protein transport / Neurexins and neuroligins / Unblocking of NMDA receptors, glutamate binding and activation / clustering of voltage-gated potassium channels / anterograde axonal protein transport / RAF/MAP kinase cascade / structural constituent of postsynaptic density / cellular response to potassium ion / axon initial segment / juxtaparanode region of axon ...retrograde axonal protein transport / Neurexins and neuroligins / Unblocking of NMDA receptors, glutamate binding and activation / clustering of voltage-gated potassium channels / anterograde axonal protein transport / RAF/MAP kinase cascade / structural constituent of postsynaptic density / cellular response to potassium ion / axon initial segment / juxtaparanode region of axon / neurotransmitter receptor localization to postsynaptic specialization membrane / sensory perception of pain / axon cytoplasm / neuromuscular junction / kinase binding / synaptic vesicle membrane / cell junction / chemical synaptic transmission / perikaryon / postsynaptic membrane / postsynaptic density / glutamatergic synapse / nucleus / plasma membrane / cytoplasm
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 speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.028 Å
AuthorsFiorentini, M. / Kallehauge, A. / Kristensen, O. / Kastrup, J.S. / Gajhede, M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of the First Pdz Domain of Human Psd-93.
Authors: Fiorentini, M. / Nielsen, A.K. / Kristensen, O. / Kastrup, J.S. / Gajhede, M.
History
DepositionJun 22, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 19, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DISKS LARGE HOMOLOG 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,2785
Polymers10,9541
Non-polymers3244
Water2,162120
1
A: DISKS LARGE HOMOLOG 2
hetero molecules

A: DISKS LARGE HOMOLOG 2
hetero molecules

A: DISKS LARGE HOMOLOG 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,83415
Polymers32,8633
Non-polymers97112
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area5080 Å2
ΔGint-144.48 kcal/mol
Surface area14370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.198, 85.198, 45.515
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-2002-

HOH

21A-2024-

HOH

31A-2063-

HOH

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Components

#1: Protein DISKS LARGE HOMOLOG 2 / POSTSYNAPTIC DENSITY PROTEIN PSD-93 / CHANNEL-ASSOCIATED PROTEIN OF SYNAPSE-110 / CHAPSYN-110 / PSD-93


Mass: 10954.328 Da / Num. of mol.: 1 / Fragment: PDZ1, RESIDUES 95-188
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: Q91XM9, guanylate kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE FIRST 8 N-TERMINAL RESIDUES ARE CLONING ARTIFACTS REMAINING FROM THE VECTOR.

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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: 3.18 Å3/Da / Density % sol: 61.34 % / Description: NONE
Crystal growpH: 8.5 / Details: 0.01 M NICL2, 0.1 M TRIS, PH 8.5, 1 M LI2SO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 28, 2008 / Details: MIRRORS
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→28.67 Å / Num. obs: 7993 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 18.09 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 27.2
Reflection shellResolution: 2.01→2.12 Å / Redundancy: 10.6 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 8.2 / % possible all: 85.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2I1N

2i1n


Resolution: 2.028→21.747 Å / SU ML: 0.87 / σ(F): 2.28 / Phase error: 19.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2077 800 10.03 %
Rwork0.1644 --
obs0.1687 7977 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.57 Å2 / ksol: 0.408 e/Å3
Displacement parametersBiso mean: 19.36 Å2
Baniso -1Baniso -2Baniso -3
1--2.1212 Å20 Å20 Å2
2---2.1212 Å20 Å2
3---4.2423 Å2
Refinement stepCycle: LAST / Resolution: 2.028→21.747 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms735 0 16 120 871
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003770
X-RAY DIFFRACTIONf_angle_d0.7031043
X-RAY DIFFRACTIONf_dihedral_angle_d13.946291
X-RAY DIFFRACTIONf_chiral_restr0.049115
X-RAY DIFFRACTIONf_plane_restr0.002139
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0283-2.15530.20491380.16771196X-RAY DIFFRACTION99
2.1553-2.32150.25871110.16071217X-RAY DIFFRACTION100
2.3215-2.55480.21161530.16821182X-RAY DIFFRACTION100
2.5548-2.92370.21471300.17451200X-RAY DIFFRACTION100
2.9237-3.68070.18771440.16191188X-RAY DIFFRACTION100
3.6807-21.74790.18811240.14891194X-RAY DIFFRACTION99

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