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- PDB-7dtg: Crystal structure of lamin B1 Ig-like domain from human -

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Basic information

Entry
Database: PDB / ID: 7dtg
TitleCrystal structure of lamin B1 Ig-like domain from human
ComponentsLamin-B1
KeywordsNUCLEAR PROTEIN / Intermediate filament / nuclear lamin B1 / Ig-like domain
Function / homology
Function and homology information


structural constituent of nuclear lamina / Breakdown of the nuclear lamina / Depolymerization of the Nuclear Lamina / nuclear envelope organization / Nuclear Envelope Breakdown / 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 organization / Nuclear Envelope Breakdown / nuclear pore localization / lamin filament / protein localization to nuclear envelope / nuclear lamina / Initiation of Nuclear Envelope (NE) Reformation / RHOD GTPase cycle / RHOF GTPase cycle / nuclear inner membrane / Formation of Senescence-Associated Heterochromatin Foci (SAHF) / nuclear migration / Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer's disease models / phospholipase binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Meiotic synapsis / structural constituent of cytoskeleton / nuclear matrix / sequence-specific double-stranded DNA binding / nuclear envelope / heterochromatin formation / nuclear membrane / nucleoplasm / nucleus / membrane
Similarity search - Function
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
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsAhn, J. / Lee, J. / Ha, N.-C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2021
Title: Beta-strand-mediated dimeric formation of the Ig-like domains of human lamin A/C and B1.
Authors: Ahn, J. / Lee, J. / Jeong, S. / Kang, S.M. / Park, B.J. / Ha, N.C.
History
DepositionJan 5, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lamin-B1
B: Lamin-B1
C: Lamin-B1
D: Lamin-B1
F: Lamin-B1
E: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)98,0776
Polymers98,0776
Non-polymers00
Water00
1
A: Lamin-B1
E: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)32,6922
Polymers32,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Lamin-B1
F: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)32,6922
Polymers32,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Lamin-B1
D: Lamin-B1


Theoretical massNumber of molelcules
Total (without water)32,6922
Polymers32,6922
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.647, 160.751, 132.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: Protein
Lamin-B1


Mass: 16346.178 Da / Num. of mol.: 6 / Fragment: Ig-like domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LMNB1, LMN2, LMNB / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20700

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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: 3.94 Å3/Da / Density % sol: 68.75 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / Details: magnesium nitrate, PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Aug 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 17863 / % possible obs: 97.1 % / Redundancy: 7.4 % / Biso Wilson estimate: 25.16 Å2 / CC1/2: 0.997 / CC star: 0.999 / Rpim(I) all: 0.025 / Rrim(I) all: 0.08 / Net I/σ(I): 17.95
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 3.3 / Num. unique obs: 818 / CC1/2: 0.634 / CC star: 0.881 / Rpim(I) all: 0.15 / Rrim(I) all: 0.36 / % possible all: 91.1

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3UMN

3umn


Resolution: 3.6→49.83 Å / SU ML: 0.4526 / Cross valid method: FREE R-VALUE / σ(F): 1.53 / Phase error: 21.4258
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2622 1635 10 %
Rwork0.2217 14715 -
obs0.2258 16350 89.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.48 Å2
Refinement stepCycle: LAST / Resolution: 3.6→49.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 0 0 5448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00165544
X-RAY DIFFRACTIONf_angle_d0.45757512
X-RAY DIFFRACTIONf_chiral_restr0.0445852
X-RAY DIFFRACTIONf_plane_restr0.0023954
X-RAY DIFFRACTIONf_dihedral_angle_d4.685744
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.70.3731710.275632X-RAY DIFFRACTION46.96
3.7-3.820.2629810.2581732X-RAY DIFFRACTION54.27
3.82-3.960.30641240.24811112X-RAY DIFFRACTION82.73
3.96-4.120.30741390.24011259X-RAY DIFFRACTION92.34
4.12-4.30.24481490.21621343X-RAY DIFFRACTION97.77
4.3-4.530.20781500.18531349X-RAY DIFFRACTION98.55
4.53-4.810.22211480.17011331X-RAY DIFFRACTION98.53
4.81-5.180.23211530.19591372X-RAY DIFFRACTION98.77
5.19-5.710.22911510.20391359X-RAY DIFFRACTION99.41
5.71-6.530.27871510.24141371X-RAY DIFFRACTION99.28
6.53-8.220.27351560.23751394X-RAY DIFFRACTION99.55
8.22-49.830.27031620.23591461X-RAY DIFFRACTION99.57

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