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- PDB-2egk: Crystal Structure of Tamalin PDZ-Intrinsic Ligand Fusion Protein -

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Basic information

Entry
Database: PDB / ID: 2egk
TitleCrystal Structure of Tamalin PDZ-Intrinsic Ligand Fusion Protein
ComponentsGeneral receptor for phosphoinositides 1-associated scaffold protein
KeywordsPROTEIN BINDING / PDZ domain / ligand fusion
Function / homology
Function and homology information


regulation of neurotransmitter receptor transport, endosome to postsynaptic membrane / PDZ domain binding / Schaffer collateral - CA1 synapse / small GTPase binding / postsynaptic membrane / postsynaptic density / glutamatergic synapse / perinuclear region of cytoplasm / 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
PHOSPHATE ION / General receptor for phosphoinositides 1-associated scaffold protein
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.85 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 8, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms
Revision 1.4Nov 10, 2021Group: Advisory / Database references / Derived calculations
Category: database_2 / pdbx_unobs_or_zero_occ_atoms ...database_2 / pdbx_unobs_or_zero_occ_atoms / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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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
C: General receptor for phosphoinositides 1-associated scaffold protein
D: General receptor for phosphoinositides 1-associated scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,3006
Polymers45,1104
Non-polymers1902
Water77543
1
A: General receptor for phosphoinositides 1-associated scaffold protein
B: General receptor for phosphoinositides 1-associated scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6503
Polymers22,5552
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-12 kcal/mol
Surface area9620 Å2
MethodPISA
2
C: General receptor for phosphoinositides 1-associated scaffold protein
D: General receptor for phosphoinositides 1-associated scaffold protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6503
Polymers22,5552
Non-polymers951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2060 Å2
ΔGint-14 kcal/mol
Surface area9300 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7000 Å2
ΔGint-35 kcal/mol
Surface area16090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.560, 114.070, 125.740
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
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: 11277.422 Da / Num. of mol.: 4 / Fragment: PDZ domain, c-terminal peptode(Intrinsic ligand) / 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: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 3.86 Å3/Da / Density % sol: 68.13 %
Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS.
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na, 0.8M sodium dihydrogen phosphate, 0.8M potassium dihydrogen phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.97910, 0.97940, 0.99000
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97941
30.991
ReflectionResolution: 2.85→50 Å / Num. all: 31406 / Num. obs: 29994 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 5.9
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.396 / Num. unique all: 2729

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.85→50 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 199788.9 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: THE FRIEDEL PAIRS WERE USED FOR PHASING.
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 1414 5 %RANDOM
Rwork0.2687 ---
all-31406 --
obs-29994 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.879 Å2 / ksol: 0.350717 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.5 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.62 Å
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2698 0 10 43 2751
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d1.02
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: 2.85→2.95 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.269 1414 5 %
Rwork0.291 3178 -
obs-28561 90.7 %
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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