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- PDB-2ego: Crystal Structure of Tamalin PDZ Domain -

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Basic information

Entry
Database: PDB / ID: 2ego
TitleCrystal Structure of Tamalin PDZ Domain
ComponentsGeneral receptor for phosphoinositides 1-associated scaffold protein
KeywordsPROTEIN BINDING / PDZ domain / ligand-free
Function / homology
Function and homology information


regulation of postsynaptic neurotransmitter receptor internalization / PDZ domain binding / small GTPase binding / postsynaptic membrane / postsynaptic density / perinuclear region of cytoplasm / glutamatergic synapse / signal transduction / identical protein binding / plasma membrane
Similarity search - Function
: / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
General receptor for phosphoinositides 1-associated scaffold protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSugi, T. / Oyama, T. / Muto, T. / Nakanishi, S. / Morikawa, K. / Jingami, H.
CitationJournal: Embo J. / Year: 2007
Title: Crystal structures of autoinhibitory PDZ domain of Tamalin: implications for metabotropic glutamate receptor trafficking regulation
Authors: Sugi, T. / Oyama, T. / Muto, T. / Nakanishi, S. / Morikawa, K. / Jingami, H.
History
DepositionMar 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Nov 28, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: General receptor for phosphoinositides 1-associated scaffold protein
B: General receptor for phosphoinositides 1-associated scaffold protein


Theoretical massNumber of molelcules
Total (without water)21,2882
Polymers21,2882
Non-polymers00
Water1,928107
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.282, 30.034, 80.111
Angle α, β, γ (deg.)90, 132.328, 90
Int Tables number5
Space group name H-MC121

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Components

#1: Protein General receptor for phosphoinositides 1-associated scaffold protein / GRP1-associated scaffold protein / Tamalin / 95 kDa postsynaptic density protein discs-large ZO-1 ...GRP1-associated scaffold protein / Tamalin / 95 kDa postsynaptic density protein discs-large ZO-1 domain-containing protein / PSD-95 PDZ domain-containing protein


Mass: 10643.935 Da / Num. of mol.: 2 / Fragment: PDZ domain / Mutation: C135A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Tissue: brain / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8R4T5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / 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: 2.32 Å3/Da / Density % sol: 47.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350, 0.2 M potassium fluoride, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Nov 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 18424 / Num. obs: 18300 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Redundancy: 3.6 % / Biso Wilson estimate: -1 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.2
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.276 / % possible all: 97.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
CrystalClear(MSC/RIGAKU)data collection
CrystalClear(MSC/RIGAKU)data reduction
CrystalClear(MSC/RIGAKU)data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G9O

1g9o


Resolution: 1.8→41.14 Å / Rfactor Rfree error: 0.034 / Data cutoff high absF: 233285.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.267 319 5.1 %RANDOM
Rwork0.235 ---
all-18424 --
obs-18300 17.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.421173 e/Å3
Displacement parametersBiso mean: 14 Å2
Baniso -1Baniso -2Baniso -3
1-34.33 Å20 Å2-15.34 Å2
2---19.42 Å20 Å2
3----14.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.39 Å
Refinement stepCycle: LAST / Resolution: 1.8→41.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 0 107 1476
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it01.5
X-RAY DIFFRACTIONc_mcangle_it02
X-RAY DIFFRACTIONc_scbond_it02
X-RAY DIFFRACTIONc_scangle_it02.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.135 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.604 20 3.1 %
Rwork0.587 633 -
obs--11 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water.param
X-RAY DIFFRACTION3ion.param

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