3JT0 | pdb_00003jt0

Crystal Structure of the C-terminal fragment (426-558) Lamin-B1 from Homo sapiens, Northeast Structural Genomics Consortium Target HR5546A

PDB DOI: https://doi.org/10.2210/pdb3JT0/pdb

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2009-09-11 Released: 2009-09-22
Deposition Author(s): 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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.245 (Depositor), 0.256 (DCC)
R-Value Work:
0.238 (Depositor), 0.220 (DCC)
R-Value Observed:
0.238 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Northeast Structural Genomics Consortium Target HR5546A

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.

To be published.

Macromolecule Content

Total Structure Weight: 32.29 kDa
Atom Count: 1,686
Modeled Residue Count: 215
Deposited Residue Count: 288
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lamin-B1	A, B	144	Homo sapiens	Mutation(s): 0 Gene Names: LMN2, LMNB, LMNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P20700 (Homo sapiens) Explore P20700 Go to UniProtKB: P20700
PHAROS: P20700 GTEx: ENSG00000113368
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P20700
Sequence Annotations Expand
Reference Sequence

Small Molecules

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, B	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free: 0.245 (Depositor), 0.256 (DCC)
R-Value Work: 0.238 (Depositor), 0.220 (DCC)
R-Value Observed: 0.238 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.437	α = 90
b = 72.793	β = 90
c = 81.402	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
DENZO	data reduction
SCALEPACK	data scaling
PHENIX	phasing
REFMAC	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

Deposition Data

Released Date: 2009-09-22

Deposition Author(s):

Northeast Structural Genomics Consortium (NESG)

Revision History (Full details and data files)

Version 1.0: 2009-09-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Derived calculations, Refinement description
Version 1.3: 2024-10-30
Changes: Data collection, Database references, Structure summary