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- PDB-3dj1: crystal structure of TIP-1 wild type -

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Basic information

Entry
Database: PDB / ID: 3dj1
Titlecrystal structure of TIP-1 wild type
ComponentsTax1-binding protein 3
KeywordsSIGNALING PROTEIN / Tax-interacting protein-1 / PDZ domain / TIP-1 / 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 / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation / intracellular membrane-bounded organelle ...RHO GTPases Activate Rhotekin and Rhophilins / negative regulation of protein localization to cell surface / negative regulation of Wnt signaling pathway / Rho protein signal transduction / fibrillar center / beta-catenin binding / Wnt signaling pathway / actin cytoskeleton / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / 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 / MOLECULAR REPLACEMENT / Resolution: 1.8 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 ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _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: Tax1-binding protein 3
B: Tax1-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5753
Polymers27,4792
Non-polymers961
Water2,450136
1
A: Tax1-binding protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8362
Polymers13,7401
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)13,7401
Polymers13,7401
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Tax1-binding protein 3
hetero molecules

A: Tax1-binding protein 3
hetero molecules

A: Tax1-binding protein 3
hetero molecules

B: Tax1-binding protein 3

B: Tax1-binding protein 3

B: Tax1-binding protein 3


Theoretical massNumber of molelcules
Total (without water)82,7269
Polymers82,4386
Non-polymers2883
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_445-y-1,x-y-1,z1
crystal symmetry operation3_545-x+y,-x-1,z1
crystal symmetry operation4_444x-1/3,y-2/3,z-2/31
crystal symmetry operation5_444-y-1/3,x-y-2/3,z-2/31
crystal symmetry operation6_444-x+y-1/3,-x-2/3,z-2/31
Buried area11270 Å2
ΔGint-82 kcal/mol
Surface area30930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.757, 86.757, 80.321
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-144-

HOH

21B-159-

HOH

31B-188-

HOH

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Components

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


Mass: 13739.631 Da / Num. of mol.: 2
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.12 Å3/Da / Density % sol: 41.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 1.6M Ammonium sulfate, 0.1M bicine buffer, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 21968 / Num. obs: 21858 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.4 % / Biso Wilson estimate: 23.2 Å2 / Rsym value: 0.025 / Net I/σ(I): 63.3
Reflection shellResolution: 1.77→1.83 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.124 / Mean I/σ(I) obs: 13.2 / Num. unique all: 2104 / % possible all: 95.7

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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: 1.8→27.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1241665.59 / 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
Rfree0.233 2050 9.9 %RANDOM
Rwork0.215 ---
obs0.215 20752 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.8231 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--0.77 Å20 Å20 Å2
2---0.77 Å20 Å2
3---1.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1736 0 5 136 1877
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_mcbond_it1.341.5
X-RAY DIFFRACTIONc_mcangle_it2.032
X-RAY DIFFRACTIONc_scbond_it2.512
X-RAY DIFFRACTIONc_scangle_it3.762.5
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.337 357 10.6 %
Rwork0.319 3021 -
obs--97.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3so4.paramso4.top

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