3L0A | pdb_00003l0a

Crystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 A resolution

• PDB DOI: https://doi.org/10.2210/pdb3L0A/pdb

• Classification: HYDROLASE
• Organism(s): Agathobacter rectalis ATCC 33656
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-09 Released: 2010-01-12 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 
  0.250 (Depositor), 0.265 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Crystal structure of Putative exonuclease (RER070207002219) from Eubacterium rectale at 2.19 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)

Macromolecule Content 

• Total Structure Weight: 31.93 kDa 
• Atom Count: 2,263 
• Modeled Residue Count: 266 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative exonuclease	A	266	Agathobacter rectalis ATCC 33656	Mutation(s): 0  Gene Names: EUBREC_2131, RER070207002219
UniProt
Find proteins for C4ZCC6 (Agathobacter rectalis (strain ATCC 33656 / DSM 3377 / JCM 17463 / KCTC 5835 / VPI 0990)) Explore C4ZCC6  Go to UniProtKB:  C4ZCC6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PE4	D [auth A]	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL C16 H34 O8 PJWQOENWHPEPKI-UHFFFAOYSA-N
TRS	C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-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: 2.19 Å
• R-Value Free:  0.250 (Depositor), 0.265 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33L0A

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.248	α = 90
b = 88.248	β = 90
c = 69.35	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
autoSHARP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-12 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2010-01-12
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-11-01
  Changes: 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
• Version 1.5: 2024-10-30
  Changes: Data collection, Structure summary