2B2B | pdb_00002b2b

Structural distortions in psoralen cross-linked DNA

• PDB DOI: https://doi.org/10.2210/pdb2B2B/pdb
• NAKB: 2B2B

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-09-19 Released: 2006-10-03 
• Deposition Author(s): Hays, F.A., Yonggang, H., Eichman, B.F., Kong, W., Hearst, J., Ho, P.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Structural distortions in psoralen cross-linked DNA

Hays, F.A., Yonggang, H., Eichman, B.F., Kong, W., Hearst, J., Ho, P.S.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 6.7 kDa 
• Atom Count: 628 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*CP*TP*AP*GP*CP*GP*G)-3'	A, B	10	N/A

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PSO	G [auth A]	4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN C15 H14 O4 RGJSDHXSAKMPNM-UHFFFAOYSA-N
SPM	C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
CA	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA	D [auth A], F [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.262 (Depositor), 0.261 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.007	α = 90
b = 22.496	β = 128.8
c = 44.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-10-03 
Deposition Author(s): Hays, F.A., Yonggang, H., Eichman, B.F., Kong, W., Hearst, J., Ho, P.S.

Revision History  

• Version 1.0: 2006-10-03
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description