5D8F | pdb_00005d8f

crystal structure of SSB and ssDNA complex from homo sapiens

• PDB DOI: https://doi.org/10.2210/pdb5D8F/pdb
• NAKB: 5D8F

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-08-17 Released: 2016-08-17 
• Deposition Author(s): Li, Y.H., Gao, Z.Q., Dong, Y.H.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.251 (DCC) 
• R-Value Observed: 
  0.241 (Depositor) 

Starting Model: experimental

Literature

crystal structure of SSB and ssDNA complex from homo sapiens

Li, Y.H., Gao, Z.Q., Dong, Y.H.

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 and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 28.93 kDa 
• Atom Count: 1,774 
• Modeled Residue Count: 220 
• Deposited Residue Count: 240 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SOSS complex subunit B1	A, B	115	Homo sapiens	Mutation(s): 0  Gene Names: NABP2, OBFC2B, SSB1, LP3587
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BQ15 (Homo sapiens) Explore Q9BQ15  Go to UniProtKB:  Q9BQ15
PHAROS:  Q9BQ15 GTEx:  ENSG00000139579

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*TP*TP*TP*TP*TP*TP*TP*TP*TP*T)-3')	C	10	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D [auth A], E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.282 (Depositor), 0.285 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.251 (DCC) 
• R-Value Observed: 0.241 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.821	α = 90
b = 83.821	β = 90
c = 159.315	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Li, Y.H., Gao, Z.Q., Dong, Y.H.

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description