2E42 | pdb_00002e42

Crystal structure of C/EBPbeta Bzip homodimer V285A mutant bound to A High Affinity DNA fragment

• PDB DOI: https://doi.org/10.2210/pdb2E42/pdb
• NAKB: 2E42

• Classification: TRANSCRIPTION/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2006-12-01 Released: 2007-12-18 
• Deposition Author(s): Tahirov, T.H., Inoue-Bungo, T., Sato, K., Shiina, M., Hamada, K., Ogata, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 
  0.232 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Flexible Base Recognition by C/Ebpbeta

Tahirov, T.H., Inoue-Bungo, T., Sato, K., Shiina, M., Hamada, K., Ogata, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 28.5 kDa 
• Atom Count: 2,097 
• Modeled Residue Count: 164 
• Deposited Residue Count: 188 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
CCAAT/enhancer-binding protein beta	C [auth A], D [auth B]	78	Homo sapiens	Mutation(s): 1  Gene Names: CEBPB, TCF5
UniProt & NIH Common Fund Data Resources
Find proteins for P17676 (Homo sapiens) Explore P17676  Go to UniProtKB:  P17676
PHAROS:  P17676 GTEx:  ENSG00000172216

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*DTP*DAP*DGP*DGP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DAP*DT)-3')	A [auth C]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*DAP*DAP*DTP*DAP*DTP*DTP*DGP*DCP*DGP*DCP*DAP*DAP*DTP*DCP*DCP*DT)-3')	B [auth D]	16	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.252 (Depositor), 0.253 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.233 (DCC) 
• R-Value Observed: 0.232 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.881	α = 90
b = 113.319	β = 90
c = 74.439	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-12-18 
Deposition Author(s): Tahirov, T.H., Inoue-Bungo, T., Sato, K., Shiina, M., Hamada, K., Ogata, K.

Revision History  

• Version 1.0: 2007-12-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2021-11-10
  Changes: Advisory, Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description