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- PDB-1a1x: CRYSTAL STRUCTURE OF MTCP-1 INVOLVED IN T CELL MALIGNANCIES -

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Basic information

Entry
Database: PDB / ID: 1a1x
TitleCRYSTAL STRUCTURE OF MTCP-1 INVOLVED IN T CELL MALIGNANCIES
ComponentsHMTCP-1
KeywordsPROTO-ONCOGENE / MTCP-1 / ONCOGENE INVOLVED IN T CELL MALIGNANCIES
Function / homology
Function and homology information


protein serine/threonine kinase activator activity / intracellular signal transduction / protein kinase binding
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MAD PHASING / Resolution: 2 Å
AuthorsFu, Z.Q. / Dubois, G.C. / Song, S.P. / Kulikovskaya, I. / Virgilio, L. / Rothstein, J. / Croce, C.M. / Weber, I.T. / Harrison, R.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 1998
Title: Crystal structure of MTCP-1: implications for role of TCL-1 and MTCP-1 in T cell malignancies.
Authors: Fu, Z.Q. / Du Bois, G.C. / Song, S.P. / Kulikovskaya, I. / Virgilio, L. / Rothstein, J.L. / Croce, C.M. / Weber, I.T. / Harrison, R.W.
History
DepositionDec 18, 1997Processing site: BNL
Revision 1.0May 27, 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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HMTCP-1


Theoretical massNumber of molelcules
Total (without water)12,6271
Polymers12,6271
Non-polymers00
Water43224
1
A: HMTCP-1

A: HMTCP-1


Theoretical massNumber of molelcules
Total (without water)25,2542
Polymers25,2542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)62.665, 62.665, 85.962
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein HMTCP-1


Mass: 12627.200 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P56278
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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 Å3/Da / Density % sol: 37 %
Crystal growpH: 7.8
Details: PROTEIN WAS CRYSTALLIZED FROM 1.5M AMS WITH TRIZMA BUFFER AT PH 7.8
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15.0 mg/mlprotein1drop
21.5 Mammonium sulfate1reservoir
31.0 mM2-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Sep 1, 1997
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→21 Å / Num. obs: 7194 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rsym value: 0.047 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.07 Å / Redundancy: 5.4 % / Mean I/σ(I) obs: 7.6 / Rsym value: 0.147 / % possible all: 99.3
Reflection
*PLUS
Rmerge(I) obs: 0.047
Reflection shell
*PLUS
% possible obs: 99.3 % / Rmerge(I) obs: 0.147

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Processing

Software
NameVersionClassification
MADSYSphasing
X-PLOR3.8model building
X-PLOR3.8refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.8phasing
RefinementMethod to determine structure: MAD PHASING / Resolution: 2→6.5 Å / Rfactor Rfree error: 0.01 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.253 582 8.6 %RANDOM
Rwork0.211 ---
obs0.211 6733 99.7 %-
Displacement parametersBiso mean: 22.01 Å2
Refinement stepCycle: LAST / Resolution: 2→6.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms881 0 0 24 905
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.007
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_deg1.396
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.92
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.192
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.1571.5
X-RAY DIFFRACTIONx_mcangle_it3.3192
X-RAY DIFFRACTIONx_scbond_it4.212
X-RAY DIFFRACTIONx_scangle_it6.2312.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.268 73 8.7 %
Rwork0.255 739 -
obs--99.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2TIP3P.PARAMETERTIP3P.TOPOLOGY
Software
*PLUS
Name: X-PLOR / Version: 3.8 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.92
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.192
LS refinement shell
*PLUS
Rfactor obs: 0.255

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