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- PDB-1jsg: CRYSTAL STRUCTURE OF P14TCL1, AN ONCOGENE PRODUCT INVOLVED IN T-C... -

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Basic information

Entry
Database: PDB / ID: 1jsg
TitleCRYSTAL STRUCTURE OF P14TCL1, AN ONCOGENE PRODUCT INVOLVED IN T-CELL PROLYMPHOCYTIC LEUKEMIA, REVEALS A NOVEL B-BARREL TOPOLOGY
ComponentsONCOGENE PRODUCT P14TCL1
KeywordsPROTO-ONCOGENE / CL1 GENE / T CELL LEUKEMIA / ONCOPROTEIN / MICROSOME
Function / homology
Function and homology information


multicellular organism development / positive regulation of mitochondrial membrane potential / protein serine/threonine kinase activator activity / positive regulation of protein-containing complex assembly / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding ...multicellular organism development / positive regulation of mitochondrial membrane potential / protein serine/threonine kinase activator activity / positive regulation of protein-containing complex assembly / positive regulation of protein serine/threonine kinase activity / positive regulation of peptidyl-serine phosphorylation / cellular response to tumor necrosis factor / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / endoplasmic reticulum / protein-containing complex / nucleoplasm / identical protein binding / cytosol
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsHoh, F. / Yang, Y.-S. / Guignard, L. / Padilla, A. / Stern, R.-H. / Lhoste, J.-M. / Van Tilbeurgh, H.
CitationJournal: Structure / Year: 1998
Title: Crystal structure of p14TCL1, an oncogene product involved in T-cell prolymphocytic leukemia, reveals a novel beta-barrel topology.
Authors: Hoh, F. / Yang, Y.S. / Guignard, L. / Padilla, A. / Stern, M.H. / Lhoste, J.M. / van Tilbeurgh, H.
History
DepositionDec 3, 1997Processing site: BNL
Revision 1.0Mar 18, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ONCOGENE PRODUCT P14TCL1


Theoretical massNumber of molelcules
Total (without water)13,4761
Polymers13,4761
Non-polymers00
Water88349
1
A: ONCOGENE PRODUCT P14TCL1

A: ONCOGENE PRODUCT P14TCL1


Theoretical massNumber of molelcules
Total (without water)26,9512
Polymers26,9512
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
Unit cell
Length a, b, c (Å)38.897, 82.839, 117.726
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
DetailsP14 IS INVOLVED IN RARE FORMS OF LEUKEMIA BUT ITS CELLULAR ROLE REMAINS UNKNOWN. THERE EXISTS EVIDENCE FOR DIMER FORMATION IN SOLUTION BUT THE PROTEIN IS PRESENT AS A MONOMER IN THE ASYMMETRIC UNIT. A TIGHT DIMER CONTACT IS GENERATED BY THE TWO-FOLD CRYSTAL C-AXIS.

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Components

#1: Protein ONCOGENE PRODUCT P14TCL1


Mass: 13475.537 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: T-CELL / References: UniProt: P56279
#2: Water ChemComp-HOH / water / 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

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Sample preparation

CrystalDensity Matthews: 3.52 Å3/Da / Density % sol: 65.02 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.2 mMprotein1drop
25 mMTris-HCl1drop
325 mMsodium acetate1dropcan be replaced by Succinate

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionBiso Wilson estimate: 37 Å2
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 40 Å / Num. obs: 6870 / % possible obs: 99.4 % / Redundancy: 8.8 % / Num. measured all: 60407 / Rmerge(I) obs: 0.099
Reflection shell
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 2.6 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.288

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Processing

Software
NameVersionClassification
X-PLOR3.851model building
X-PLOR3.851refinement
X-PLOR3.851phasing
RefinementResolution: 2.5→8 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.259 729 11 %RANDOM
Rwork0.192 ---
obs0.192 6644 99.6 %-
Displacement parametersBiso mean: 29.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.37 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 0 50 974
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.006
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d31
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.68
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.5→2.65 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 100 9.2 %
Rwork0.285 986 -
obs--99.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg31
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.68

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