4HCB | pdb_00004hcb

The metal-free form of crystal structure of E.coli ExoI-ssDNA complex

• PDB DOI: https://doi.org/10.2210/pdb4HCB/pdb
• NAKB: 4HCB

• Classification: HYDROLASE/DNA
• Organism(s): Escherichia coli DH5[alpha]
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-09-29 Released: 2013-10-09 
• Deposition Author(s): Qiu, R., Wei, J., Lou, T., Liu, M., Ji, C., Gong, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

The structures of Escherichia coli exonuclease I in complex with the single strand DNA

Qiu, R., Lou, T., Wei, J., Liu, M., Gu, S., Tang, R., Ji, C., Gong, W.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 119.23 kDa 
• Atom Count: 8,562 
• Modeled Residue Count: 947 
• Deposited Residue Count: 986 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease I	A, B	481	Escherichia coli DH5[alpha]	Mutation(s): 0  Gene Names: b2011, cpeA, JW1993, sbcB, xonA EC: 3.1.11.1
UniProt
Find proteins for P04995 (Escherichia coli (strain K12)) Explore P04995  Go to UniProtKB:  P04995

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*AP*A)-3')	C, D	12	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], O [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], J [auth B], K [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.224 (Depositor), 0.222 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.544	α = 90
b = 107.289	β = 90
c = 157.574	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-09 
Deposition Author(s): Qiu, R., Wei, J., Lou, T., Liu, M., Ji, C., Gong, W.

Revision History  

• Version 1.0: 2013-10-09
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description