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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.262 (Depositor), 0.260 (DCC)
R-Value Work:
0.210 (Depositor), 0.210 (DCC)
R-Value Observed:
0.215 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

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.

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

Find similar nucleic acids by: Sequence | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(CPCPGPCPTPAPGPCPGPG)-3'	A, B	10	N/A
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PSO Query on PSO Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4'-HYDROXYMETHYL-4,5',8-TRIMETHYLPSORALEN C₁₅ H₁₄ O₄ RGJSDHXSAKMPNM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain H [auth B] MOL2 format, chain E [auth A] MOL2 format, chain H [auth B] mmCIF format, chain E [auth A] mmCIF format, chain H [auth B]	E [auth A], H [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain H [auth B] Interactions & Density Focus chain E [auth A] Focus chain H [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain I [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain I [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain I [auth B]	D [auth A], F [auth A], I [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth A] Focus chain I [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.262 (Depositor), 0.260 (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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-10-03

Deposition Author(s):

Revision History (Full details and data files)

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