3LYB

Structure of putative endoribonuclease(KP1_3112) from Klebsiella pneumoniae

• PDB DOI: https://doi.org/10.2210/pdb3LYB/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-02-26 Released: 2010-03-23 
• Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 

Literature

Structure of putative endoribonuclease(KP1_3112) from Klebsiella pneumoniae

Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C.

To be published.

Biological Assembly 1  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

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

Biological Assembly 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 73.88 kDa 
• Atom Count: 4,290 
• Modelled Residue Count: 542 
• Deposited Residue Count: 660 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative endoribonuclease	A, B, C, D	165	Klebsiella pneumoniae subsp. pneumoniae NTUH-K2044	Mutation(s): 0  Gene Names: KP1_3112

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth A], F [auth B], G [auth B], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.66 Å
• R-Value Free: 0.248 
• R-Value Work: 0.193 
• R-Value Observed: 0.195 
• Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 166.557	α = 90
b = 166.557	β = 90
c = 166.557	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
HKL-2000	data reduction
PHENIX	phasing
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-03-23 
Deposition Author(s): Ramagopal, U.A., Toro, R., Burley, S.K., Almo, S.C., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2010-03-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2021-02-10
  Changes: Database references, Derived calculations, Structure summary