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- PDB-1jnp: Crystal Structure of Murine Tcl1 at 2.5 Resolution -

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Basic information

Entry
Database: PDB / ID: 1jnp
TitleCrystal Structure of Murine Tcl1 at 2.5 Resolution
ComponentsT-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A
KeywordsIMMUNE SYSTEM / BETA BARREL / DIMER
Function / homology
Function and homology information


ooplasm / regulation of stem cell population maintenance / pronucleus / somatic stem cell population maintenance / activation of protein kinase B activity / protein serine/threonine kinase activator activity / cell cortex / negative regulation of gene expression / endoplasmic reticulum / nucleus
Similarity search - Function
Proto-oncogene - Oncogene Product P14tcl1 / TCL1/MTCP1 / TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
T-cell leukemia/lymphoma protein 1A
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsPetock, J.M. / Torshin, I.Y. / Wang, Y.F. / DuBois, G.C. / Croce, C.M. / Harrison, R.W. / Weber, I.T.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Structure of murine Tcl1 at 2.5 A resolution and implications for the TCL oncogene family.
Authors: Petock, J.M. / Torshin, I.Y. / Wang, Y.F. / Du Bois, G.C. / Croce, C.M. / Harrison, R.W. / Weber, I.T.
History
DepositionJul 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Advisory / Data collection / Experimental preparation
Category: diffrn / exptl_crystal_grow / pdbx_unobs_or_zero_occ_atoms
Item: _diffrn.ambient_temp / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp
Revision 1.4Oct 27, 2021Group: Advisory / Database references
Category: database_2 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.5Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: T-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A
B: T-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A


Theoretical massNumber of molelcules
Total (without water)28,1962
Polymers28,1962
Non-polymers00
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)89.323, 115.911, 37.945
Angle α, β, γ (deg.)90.00, 115.15, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein T-CELL LEUKEMIA/LYMPHOMA PROTEIN 1A / P14 TCL1 PROTEIN / TCL1 ONCOGENE / TCL-1 PROTEIN


Mass: 14098.037 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P56280
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.83 Å3/Da / Density % sol: 60.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 3.9
Details: Sodium Acetate, Tris, 1-O-octyl-beta-D-glucopyranoside, pH 3.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15 mg/mlprotein1drop
210 mMTris1drop
30.05 Msodium acetate1reservoir
40.1 MTris1reservoir

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 1.037
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 11, 1999
RadiationMonochromator: Double Flat Crystal Fixed-exit Monochromator, Si 111
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.5→25 Å / Num. all: 11802 / Num. obs: 11802 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Rsym value: 0.058 / Net I/σ(I): 11.6
Reflection shellResolution: 2.5→2.54 Å / Rsym value: 0.264 / % possible all: 94.7
Reflection
*PLUS
Lowest resolution: 10 Å / Num. obs: 11019 / % possible obs: 99.8 % / Num. measured all: 11802 / Rmerge(I) obs: 0.059
Reflection shell
*PLUS
Lowest resolution: 2.59 Å / % possible obs: 99.5 %

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→10 Å / Num. parameters: 1813 / Num. restraintsaints: 2096 / Cross valid method: FREE R / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.2356 606 -RANDOM
Rwork0.2256 ---
all0.196 11625 --
obs0.2257 11802 92.1 %-
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 1803
Refinement stepCycle: LAST / Resolution: 2.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1754 0 0 49 1803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0
X-RAY DIFFRACTIONs_angle_d0
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0
X-RAY DIFFRACTIONs_zero_chiral_vol0
X-RAY DIFFRACTIONs_non_zero_chiral_vol0
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.048
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.094
X-RAY DIFFRACTIONs_approx_iso_adps0
Software
*PLUS
Name: SHELXL-97 / Classification: refinement
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor all: 0.2257 / Rfactor Rwork: 0.196
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.019
X-RAY DIFFRACTIONs_angle_d
X-RAY DIFFRACTIONs_angle_deg2.1

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