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- PDB-1q3o: Crystal structure of the Shank PDZ-ligand complex reveals a class... -

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Basic information

Entry
Database: PDB / ID: 1q3o
TitleCrystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization
ComponentsShank1
KeywordsPEPTIDE BINDING PROTEIN / shank / pdz / gkap
Function / homology
Function and homology information


somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse ...somatostatin receptor binding / determination of affect / synaptic receptor adaptor activity / olfactory behavior / synapse maturation / Neurexins and neuroligins / negative regulation of actin filament bundle assembly / structural constituent of postsynaptic density / righting reflex / protein localization to synapse / vocalization behavior / habituation / regulation of AMPA receptor activity / ankyrin repeat binding / dendritic spine morphogenesis / positive regulation of dendritic spine development / adult behavior / social behavior / positive regulation of excitatory postsynaptic potential / associative learning / neuromuscular process controlling balance / excitatory synapse / long-term memory / ionotropic glutamate receptor binding / G protein-coupled receptor binding / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / SH3 domain binding / signaling receptor complex adaptor activity / postsynaptic membrane / scaffold protein binding / protein-containing complex assembly / dendritic spine / postsynaptic density / neuron projection / dendrite / glutamatergic synapse / synapse / protein-containing complex binding / membrane / identical protein binding / plasma membrane / cytosol
Similarity search - Function
PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily ...PDZ domain 6 / PDZ domain / Variant SH3 domain / SAM domain (Sterile alpha motif) / PDZ domain / Pdz3 Domain / SAM domain profile. / Sterile alpha motif. / Sterile alpha motif domain / Sterile alpha motif/pointed domain superfamily / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / Ankyrin repeats (3 copies) / PDZ superfamily / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / Mainly Beta
Similarity search - Domain/homology
BROMIDE ION / SH3 and multiple ankyrin repeat domains protein 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsIm, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H.
CitationJournal: J.Biol.Chem. / Year: 2003
Title: Crystal structure of the Shank PDZ-ligand complex reveals a class I PDZ interaction and a novel PDZ-PDZ dimerization
Authors: Im, Y.J. / Lee, J.H. / Park, S.H. / Park, S.J. / Rho, S.-H. / Kang, G.B. / Kim, E. / Eom, S.H.
History
DepositionJul 31, 2003Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 27, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: Shank1
B: Shank1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5477
Polymers24,1482
Non-polymers4005
Water1,69394
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.000, 50.340, 51.770
Angle α, β, γ (deg.)90.00, 106.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Shank1 /


Mass: 12073.959 Da / Num. of mol.: 2 / Fragment: PDZ domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: shank1a / Plasmid: pGEX4T1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9WV48
#2: Chemical
ChemComp-BR / BROMIDE ION / Bromide


Mass: 79.904 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Br
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 94 / 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: 2.18 Å3/Da / Density % sol: 43.11 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: PEG 20K, NaBr, Glycerol, Sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
pH: 7.4 / Method: vapor diffusion, hanging drop / Details: Park, S.H., (2002) Acta Cryst., D58, 1353.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
112 mg/mlprotein1drop
250 mMTris-HCl1droppH7.4
310 %(w/v)PEG200001reservoir
40.2 M1reservoirNaBr
520 %(v/v)glycerol1reservoir
6100 mMsodium acetate1reservoirpH4.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11101
21
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B10.9205
SYNCHROTRONPhoton Factory BL-18B20.9201
SYNCHROTRONPhoton Factory BL-18B30.918
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 13, 2000 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.92051
20.92011
30.9181
ReflectionResolution: 1.8→27.7 Å / Num. all: 58984 / Num. obs: 58394 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 3 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 13.8
Reflection shellResolution: 1.8→1.89 Å / Redundancy: 3 % / Rmerge(I) obs: 0.377 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.377 / % possible all: 99
Reflection shell
*PLUS
% possible obs: 99 %

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→27.73 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 708448.89 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 934 4.9 %RANDOM
Rwork0.234 ---
all0.235 19164 --
obs0.234 19150 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.4534 Å2 / ksol: 0.379267 e/Å3
Displacement parametersBiso mean: 32.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.92 Å20 Å22.98 Å2
2---2.18 Å20 Å2
3----0.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1623 0 5 94 1722
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.69
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 154 4.8 %
Rwork0.334 3031 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.1
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.69

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