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- PDB-1c8z: C-TERMINAL DOMAIN OF MOUSE BRAIN TUBBY PROTEIN -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1c8z
TitleC-TERMINAL DOMAIN OF MOUSE BRAIN TUBBY PROTEIN
ComponentsTUBBY PROTEIN
KeywordsSIGNALING PROTEIN / TUBBY FILLED-BARREL / BETA-BARREL / FILLED-BETA-ROLL / 12-STRANDED-BETA-BARREL / HELIX-FILLED-BARREL / OBESITY BLINDNESS / DEAFNESS
Function / homology
Function and homology information


intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / protein localization to cilium / photoreceptor cell maintenance / response to stimulus / positive regulation of phagocytosis ...intraciliary transport particle A binding / protein localization to photoreceptor outer segment / receptor localization to non-motile cilium / intraciliary transport / phagocytosis, recognition / regulation of G protein-coupled receptor signaling pathway / protein localization to cilium / photoreceptor cell maintenance / response to stimulus / positive regulation of phagocytosis / G protein-coupled receptor binding / sensory perception of sound / cilium / retina development in camera-type eye / protein-containing complex binding / extracellular region / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tubby Protein; Chain A / Tubby Protein; Chain A / Tubby, N-terminal / Tubby N-terminal / Tubby, C-terminal / Tubby, C-terminal, conserved site / Tub family / Tub family signature 1. / Tub family signature 2. / Tubby-like, C-terminal ...Tubby Protein; Chain A / Tubby Protein; Chain A / Tubby, N-terminal / Tubby N-terminal / Tubby, C-terminal / Tubby, C-terminal, conserved site / Tub family / Tub family signature 1. / Tub family signature 2. / Tubby-like, C-terminal / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / Tubby protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsBoggon, T.J. / Myers, S.C. / Shapiro, L.
CitationJournal: Science / Year: 1999
Title: Implication of tubby proteins as transcription factors by structure-based functional analysis.
Authors: Boggon, T.J. / Shan, W.S. / Santagata, S. / Myers, S.C. / Shapiro, L.
History
DepositionJul 30, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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: TUBBY PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1863
Polymers29,9961
Non-polymers1902
Water9,170509
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.536, 51.023, 121.074
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein TUBBY PROTEIN /


Mass: 29996.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P50586
#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.: 509 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2% PEG 4000, 0.1M HEPES, 4% 2-PROPANOL, 5MM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP at 293K
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
210 mMTris1drop
30.15 M1dropNaCl
45 mMdithiothreitol1drop
52 %PEG40001reservoir
60.1 MHEPES1reservoir
74 %2-propanol1reservoir
85 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9537
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 30, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / % possible obs: 98 % / Redundancy: 5 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 30.26
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5 % / Rmerge(I) obs: 0.143 / % possible all: 93.3
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 21512 / Num. measured all: 569516
Reflection shell
*PLUS
% possible obs: 93.3 %

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Processing

Software
NameClassification
SHARPphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→8 Å / σ(F): 3 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.265 937 4.9 %RANDOM
Rwork0.2102 ---
all0.2102 20231 --
obs0.2102 19244 89 %-
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 10 509 2732
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.64
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 8 Å / σ(F): 3 / % reflection Rfree: 4.9 %
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
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.64

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