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- PDB-2z15: Crystal structure of human Tob1 protein -

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Basic information

Entry
Database: PDB / ID: 2z15
TitleCrystal structure of human Tob1 protein
ComponentsProtein Tob1
KeywordsSIGNALING PROTEIN / human Tob1 protein / Phosphorylation / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of SMAD protein signal transduction / CCR4-NOT complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / SMAD binding / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / receptor tyrosine kinase binding / transcription corepressor activity ...negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of SMAD protein signal transduction / CCR4-NOT complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / SMAD binding / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / receptor tyrosine kinase binding / transcription corepressor activity / regulation of gene expression / negative regulation of translation / negative regulation of cell population proliferation / nucleus / cytoplasm
Similarity search - Function
Tob1/2 / Anti-proliferative protein, N-terminal domain / BTG family signature 1. / BTG family signature 2. / Anti-proliferative protein / BTG-like domain superfamily / BTG family / tob/btg1 family / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSaito, K. / Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of human Tob1 protein
Authors: Saito, K. / Kishishita, S. / Nishino, A. / Murayama, K. / Terada, T. / Shirouzu, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 8, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 13, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Protein Tob1
B: Protein Tob1
C: Protein Tob1
D: Protein Tob1


Theoretical massNumber of molelcules
Total (without water)58,5464
Polymers58,5464
Non-polymers00
Water8,215456
1
A: Protein Tob1


Theoretical massNumber of molelcules
Total (without water)14,6361
Polymers14,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein Tob1


Theoretical massNumber of molelcules
Total (without water)14,6361
Polymers14,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein Tob1


Theoretical massNumber of molelcules
Total (without water)14,6361
Polymers14,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein Tob1


Theoretical massNumber of molelcules
Total (without water)14,6361
Polymers14,6361
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.064, 121.162, 152.553
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
Protein Tob1 / Transducer of erbB-2 1


Mass: 14636.484 Da / Num. of mol.: 4 / Fragment: UNP residues 1-117
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: TOB1, TOB, TROB1 / Plasmid: PK051011-08 / References: UniProt: P50616
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / 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: 2.85 Å3/Da / Density % sol: 56.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 0.1M Sodium acetate trihydrate, 8% PEG4000, pH4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9789, 0.9794, 0.964
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 6, 2006 / Details: mirrors
RadiationMonochromator: Si II / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97891
20.97941
30.9641
ReflectionResolution: 2.3→50 Å / Num. obs: 30540 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 6.76 % / Biso Wilson estimate: 13.7 Å2 / Rsym value: 0.08 / Net I/σ(I): 21.6
Reflection shellResolution: 2.3→2.42 Å / Mean I/σ(I) obs: 4.94 / Rsym value: 0.25 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.3→47.44 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 70689.48 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1527 5 %RANDOM
Rwork0.194 ---
obs0.194 30007 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 43.413 Å2 / ksol: 0.359178 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.88 Å20 Å20 Å2
2--3.93 Å20 Å2
3---0.95 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3882 0 0 456 4338
Refine LS restraints
Refine-IDTypeDev ideal
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.77
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
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.279 423 5 %
Rwork0.227 8044 -
obs--88.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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