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- PDB-2v0x: The dimerization domain of LAP2alpha -

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Basic information

Entry
Database: PDB / ID: 2v0x
TitleThe dimerization domain of LAP2alpha
ComponentsLAMINA-ASSOCIATED POLYPEPTIDE 2 ISOFORMS ALPHA/ZETA
KeywordsCELL CYCLE / ALTERNATIVE SPLICING / LAMINA-ASSOCIATED POLYPEPTIDE / NUCLEAR PROTEIN / PHOSPHORYLATION / CHROMOSOMAL PROTEIN / LAMIN A / COILED COIL / DNA-BINDING / LAMINOPATHY
Function / homology
Function and homology information


nuclear inner membrane / nuclear envelope / nuclear membrane / chromatin / regulation of DNA-templated transcription / DNA binding / identical protein binding / nucleus
Similarity search - Function
Helix Hairpins - #3160 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / LEM domain / LEM domain / LEM domain profile. ...Helix Hairpins - #3160 / LEM-like domain / Lamina-associated polypeptide 2 alpha, C-terminal / Thymopoietin protein / Lamina-associated polypeptide 2 alpha / LEM-like domain profile. / Thymopoietin / LEM domain / LEM domain / LEM domain profile. / in nuclear membrane-associated proteins / LEM/LEM-like domain superfamily / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Lamina-associated polypeptide 2, isoforms alpha/zeta
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsBradley, C.M. / Jones, S. / Huang, Y. / Suzuki, Y. / Kvaratskhelia, M. / Hickman, A.B. / Craigie, R. / Dyda, F.
CitationJournal: Structure / Year: 2007
Title: Structural Basis for Dimerization of Lap2Alpha, a Component of the Nuclear Lamina.
Authors: Bradley, C.M. / Jones, S. / Huang, Y. / Suzuki, Y. / Kvaratskhelia, M. / Hickman, A.B. / Craigie, R. / Dyda, F.
History
DepositionMay 20, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 6, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 15, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LAMINA-ASSOCIATED POLYPEPTIDE 2 ISOFORMS ALPHA/ZETA
B: LAMINA-ASSOCIATED POLYPEPTIDE 2 ISOFORMS ALPHA/ZETA


Theoretical massNumber of molelcules
Total (without water)51,0892
Polymers51,0892
Non-polymers00
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)55.084, 55.683, 122.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.1598, 0.0151, -0.987), (0.0281, -0.9994, -0.0198), (-0.9868, -0.0309, 0.1592)
Vector: 29.8832, 47.8725, 26.6981)

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Components

#1: Protein LAMINA-ASSOCIATED POLYPEPTIDE 2 ISOFORMS ALPHA/ZETA / THYMOPOIETIN ISOFORMS ALPHA/ZETA / TP ALPHA/ZETA / LAMINA ASSOCIATED POLYPEPTIDE 2ALPHA


Mass: 25544.535 Da / Num. of mol.: 2 / Fragment: DIMERIZATION DOMAIN, RESIDUES 458-692 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET-16B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q61033
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ARG 548 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 605 TO ASP ...ENGINEERED RESIDUE IN CHAIN A, ARG 548 TO ALA ENGINEERED RESIDUE IN CHAIN A, ILE 605 TO ASP ENGINEERED RESIDUE IN CHAIN B, ARG 548 TO ALA ENGINEERED RESIDUE IN CHAIN B, ILE 605 TO ASP
Sequence detailsR549A, I606D ENGINEERED POINT MUTATIONS

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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: 1.84 Å3/Da / Density % sol: 32 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 6.5
Details: VAPOR DIFFUSION AT 4C. PROTEIN CONCENTRATION: 8.5 MG/ML PROTEIN BUFFER: 25MM NAACETATE, PH 5.0 0.5 M NACL 1 MM EDTA 5 MM B-ME PRECIPITANT: 25% (W/V) PEG 3K 0.1 M MES PH 6.5 10 MM TRIS PH 8.5 5 MM B-ME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.968626
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 12, 2005 / Details: SAGITALLY FOCUSING MONOCHROMATOR, FOCUSING MIRROR
RadiationMonochromator: SI(220) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.968626 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 20002 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 7.15 % / Biso Wilson estimate: 41 Å2 / Rmerge(I) obs: 0.01 / Net I/σ(I): 8.9
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 7.39 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2005refinement
HKL-2000data reduction
HKL-2000data scaling
PHASESphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→30 Å / Rfactor Rfree error: 0.01 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.257 947 4.8 %RANDOM
Rwork0.2126 ---
obs-19535 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.71 Å2 / ksol: 0.341419 e/Å3
Displacement parametersBiso mean: 51.2 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3030 0 0 59 3089
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007437
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_deg1.37936
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPH19_MOD.SOL

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