4RUW | pdb_00004ruw

The crystal structure of endonuclease/exonuclease/phosphatase from Beutenbergia cavernae DSM 12333

• PDB DOI: https://doi.org/10.2210/pdb4RUW/pdb

• Classification: HYDROLASE
• Organism(s): Beutenbergia cavernae DSM 12333
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-11-23 Released: 2014-12-24 
• Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free: 
  0.148 (Depositor), 0.159 (DCC) 
• R-Value Work: 
  0.138 (Depositor) 
• R-Value Observed: 
  0.138 (Depositor) 

Literature

The crystal structure of endonuclease/exonuclease/phosphatase from Beutenbergia cavernae DSM 12333

Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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)

Macromolecule Content 

• Total Structure Weight: 46.64 kDa 
• Atom Count: 3,460 
• Modeled Residue Count: 386 
• Deposited Residue Count: 440 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Endonuclease/exonuclease/phosphatase	A	440	Beutenbergia cavernae DSM 12333	Mutation(s): 0  Gene Names: Bcav_3678 EC: 3.1.4
UniProt
Find proteins for C5C3L1 (Beutenbergia cavernae (strain ATCC BAA-8 / DSM 12333 / CCUG 43141 / JCM 11478 / NBRC 16432 / NCIMB 13614 / HKI 0122)) Explore C5C3L1  Go to UniProtKB:  C5C3L1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Modified Residue	Modification Type	Formula	2D Diagram
MSE	A	MET	Selenomethionine	C5 H11 N O2 Se

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.28 Å
• R-Value Free:  0.148 (Depositor), 0.159 (DCC) 
• R-Value Work:  0.138 (Depositor) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.995	α = 90
b = 81.121	β = 95.91
c = 46.854	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
MLPHARE	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-24 
Deposition Author(s): Wu, R., Jedrzejczak, R., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2014-12-24
  Type: Initial release
  
• Version 1.1: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary