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- PDB-3dj3: Crystal Structure of C-terminal Truncated TIP-1 (6-113) -

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Basic information

Entry
Database: PDB / ID: 3dj3
TitleCrystal Structure of C-terminal Truncated TIP-1 (6-113)
ComponentsTax1-binding protein 3
KeywordsSIGNALING PROTEIN / TIP-1 / PDZ domain / Cytoplasm / Nucleus / Wnt signaling pathway
Function / homology
Function and homology information


RHO GTPases Activate Rhotekin and Rhophilins / negative regulation of protein localization to cell surface / negative regulation of Wnt signaling pathway / Rho protein signal transduction / Wnt signaling pathway / fibrillar center / beta-catenin binding / actin cytoskeleton / negative regulation of cell population proliferation / nucleus ...RHO GTPases Activate Rhotekin and Rhophilins / negative regulation of protein localization to cell surface / negative regulation of Wnt signaling pathway / Rho protein signal transduction / Wnt signaling pathway / fibrillar center / beta-catenin binding / actin cytoskeleton / negative regulation of cell population proliferation / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Tax1-binding protein 3 / : / 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
Tax1-binding protein 3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsShen, Y.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural Basis of beta-Catenin Recognition by Tax-interacting Protein-1
Authors: Zhang, J. / Yan, X. / Shi, C. / Yang, X. / Guo, Y. / Tian, C. / Long, J. / Shen, Y.
History
DepositionJun 21, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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: Tax1-binding protein 3
B: Tax1-binding protein 3
C: Tax1-binding protein 3
D: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)50,0334
Polymers50,0334
Non-polymers00
Water1,856103
1
A: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)12,5081
Polymers12,5081
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)86.808, 86.808, 81.909
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Tax1-binding protein 3 / Tax interaction protein 1 / TIP-1


Mass: 12508.190 Da / Num. of mol.: 4 / Fragment: c-terminal truncation, UNP residues 1-112
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9DBG9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 3.08 Å3/Da / Density % sol: 60.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.18M DL-malic acid, 25% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.97 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Mar 2, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 23909 / Num. obs: 23790 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 36.1 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 38
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.149 / Mean I/σ(I) obs: 10 / Num. unique all: 2374 / % possible all: 98.8

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3DIW

3diw


Resolution: 2.4→26.03 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 602441.81 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.314 1044 4.8 %RANDOM
Rwork0.265 ---
obs0.265 21933 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.2045 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 37.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.41 Å20 Å20 Å2
2--0.41 Å20 Å2
3----0.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.6 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.4→26.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3119 0 0 103 3222
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.72
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.092
X-RAY DIFFRACTIONc_scbond_it1.722
X-RAY DIFFRACTIONc_scangle_it2.692.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.459 164 4.8 %
Rwork0.367 3276 -
obs--86.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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