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- PDB-3jt0: Crystal Structure of the C-terminal fragment (426-558) Lamin-B1 f... -

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Basic information

Entry
Database: PDB / ID: 3jt0
TitleCrystal Structure of the C-terminal fragment (426-558) Lamin-B1 from Homo sapiens, Northeast Structural Genomics Consortium Target HR5546A
ComponentsLamin-B1
KeywordsSTRUCTURAL PROTEIN / Structural Genomics / PSI-2 / Protein Structure Initiative / Northeast Structural Genomics Consortium / NESG / HR5546A / LMNB1_HUMAN / Lamin-B1 / Acetylation / Chromosomal rearrangement / Coiled coil / Intermediate filament / Leukodystrophy / Lipoprotein / Membrane / Nucleus / Phosphoprotein / Polymorphism / Prenylation
Function / homology
Function and homology information


structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation ...structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / Nuclear Envelope Breakdown / nuclear envelope organization / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / RHOF GTPase cycle / RHOD GTPase cycle / nuclear migration / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phospholipase binding / heterochromatin formation / Meiotic synapsis / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / structural constituent of cytoskeleton / nuclear matrix / sequence-specific double-stranded DNA binding / nuclear envelope / nuclear membrane / nucleoplasm / membrane / nucleus
Similarity search - Function
Lamin Tail domain / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. ...Lamin Tail domain / Lamin tail domain superfamily / Lamin tail domain / Lamin Tail Domain / Lamin-tail (LTD) domain profile. / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Phenix / Resolution: 2.392 Å
AuthorsKuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. ...Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Northeast Structural Genomics Consortium Target HR5546A
Authors: Kuzin, A. / Abashidze, M. / Seetharaman, J. / Sahdev, S. / Xiao, R. / Ciccosanti, C. / Belote, R.L. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionSep 11, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Refinement description
Category: software / struct_conn
Item: _software.contact_author / _software.contact_author_email ..._software.contact_author / _software.contact_author_email / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lamin-B1
B: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)32,2942
Polymers32,2942
Non-polymers00
Water37821
1
A: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)16,1471
Polymers16,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)16,1471
Polymers16,1471
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.437, 72.793, 81.402
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 Lamin-B1


Mass: 16147.178 Da / Num. of mol.: 2 / Fragment: residues 426-558
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMN2, LMNB, LMNB1 / Plasmid: BL21 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: P20700
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 1.81 Å3/Da / Density % sol: 32.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7
Details: Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 100 mM NH4H2PO4, 100 mM Hepes, 18% PEG3350, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.97908 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 6, 2009 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97908 Å / Relative weight: 1
ReflectionResolution: 2.392→30 Å / Num. obs: 17107 / % possible obs: 95.8 % / Observed criterion σ(I): -3 / Rmerge(I) obs: 0.051 / Net I/σ(I): 5.8
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.242 / Mean I/σ(I) obs: 7.7

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Processing

Software
NameVersionClassificationNB
PHENIX1.4_115refinement
PDB_EXTRACT3data extraction
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
REFMACrefinement
RefinementMethod to determine structure: Phenix / Resolution: 2.392→28.322 Å / SU ML: 0.25 / σ(F): 1.34 / Phase error: 21.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.245 447 4.79 %
Rwork0.2379 --
obs0.2383 9337 95.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.059 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 39.972 Å2
Baniso -1Baniso -2Baniso -3
1-3.369 Å20 Å20 Å2
2--0.095 Å20 Å2
3----3.464 Å2
Refinement stepCycle: LAST / Resolution: 2.392→28.322 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1665 0 0 21 1686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071693
X-RAY DIFFRACTIONf_angle_d1.3422294
X-RAY DIFFRACTIONf_dihedral_angle_d18.726609
X-RAY DIFFRACTIONf_chiral_restr0.1259
X-RAY DIFFRACTIONf_plane_restr0.007292
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3916-2.73740.26651560.26852970X-RAY DIFFRACTION99
2.7374-3.44790.26161500.2673062X-RAY DIFFRACTION100
3.4479-28.32450.22791410.21232858X-RAY DIFFRACTION89
Refinement TLS params.Method: refined / Origin x: 33.4386 Å / Origin y: 44.9057 Å / Origin z: 29.3476 Å
111213212223313233
T0.1704 Å2-0.0257 Å20.0337 Å2-0.1491 Å2-0.0293 Å2--0.1839 Å2
L0.6576 °20.5334 °20.0096 °2-1.0164 °20.0662 °2--0.2975 °2
S-0.0101 Å °0.0372 Å °-0.0042 Å °0.1385 Å °-0.0408 Å °-0.0085 Å °0.0138 Å °0.0447 Å °0.043 Å °
Refinement TLS groupSelection details: all
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water.param

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