3K93

Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3K93/pdb

• Classification: HYDROLASE
• Organism(s): Histophilus somni 129PT
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-10-15 Released: 2009-11-03 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 

Literature

Crystal structure of phage related exonuclease (YP_719632.1) from HAEMOPHILUS SOMNUS 129PT at 2.15 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 26.29 kDa 
• Atom Count: 1,948 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
phage related exonuclease	A	223	Histophilus somni 129PT	Mutation(s): 0  Gene Names: HS_1420
UniProt
Find proteins for Q0I4G3 (Histophilus somni (strain 129Pt)) Explore Q0I4G3  Go to UniProtKB:  Q0I4G3

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	F [auth A], G [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	C [auth A], D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	B [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.212 
• R-Value Work: 0.172 
• R-Value Observed: 0.174 
• Space Group: P 3 2 1
• Diffraction Data: https://doi.org/10.18430/M33K93

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.369	α = 90
b = 113.369	β = 90
c = 42.284	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-03 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2009-11-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence, Refinement description
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2023-02-01
  Changes: Database references, Derived calculations