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- PDB-8i33: Coil 1a of lamin A (residue 25-65) -

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Basic information

Entry
Database: PDB / ID: 8i33
TitleCoil 1a of lamin A (residue 25-65)
ComponentsPrelamin-A/C
KeywordsSTRUCTURAL PROTEIN / Lamin A / coil 1a / coiled-coil
Function / homology
Function and homology information


nuclear lamina / intermediate filament / nuclear matrix / nuclear envelope / nuclear speck / structural molecule activity
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: 1.62 Å
AuthorsJeong, S. / Ha, N.C.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: Coil 1a of lamin A (residue 25-65)
Authors: Jeong, S. / Ha, N.C.
History
DepositionJan 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Prelamin-A/C
B: Prelamin-A/C
C: Prelamin-A/C
D: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)19,8344
Polymers19,8344
Non-polymers00
Water1,53185
1
A: Prelamin-A/C
C: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)9,9172
Polymers9,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-16 kcal/mol
Surface area6630 Å2
MethodPISA
2
B: Prelamin-A/C
D: Prelamin-A/C


Theoretical massNumber of molelcules
Total (without water)9,9172
Polymers9,9172
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-15 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)22.933, 33.703, 49.229
Angle α, β, γ (deg.)97.280, 91.200, 94.630
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein/peptide
Prelamin-A/C


Mass: 4958.617 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: A0A6Q8PFJ0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 1.9 Å3/Da / Density % sol: 35.43 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / Details: NaCl, PEG 6000, sodium thiocyanate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 136711 / % possible obs: 96.6 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.06 Å2 / CC1/2: 0.993 / Net I/σ(I): 24.29
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 6.74 / Num. unique obs: 18503 / CC1/2: 0.977 / Rpim(I) all: 0.108 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→33.31 Å / SU ML: 0.1379 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 23.418
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 888 4.98 %
Rwork0.1967 16940 -
obs0.1982 17828 96.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.23 Å2
Refinement stepCycle: LAST / Resolution: 1.62→33.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1358 0 8 85 1451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611366
X-RAY DIFFRACTIONf_angle_d0.7091832
X-RAY DIFFRACTIONf_chiral_restr0.0459218
X-RAY DIFFRACTIONf_plane_restr0.0082244
X-RAY DIFFRACTIONf_dihedral_angle_d3.2867192
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.720.23951360.18912698X-RAY DIFFRACTION92.28
1.72-1.850.27571470.20142796X-RAY DIFFRACTION95.03
1.85-2.040.23991460.20032830X-RAY DIFFRACTION96.34
2.04-2.340.22561700.1882836X-RAY DIFFRACTION97.25
2.34-2.940.2351380.19712886X-RAY DIFFRACTION97.93
2.94-33.310.19961510.19982894X-RAY DIFFRACTION98.7

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