Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 53.78 kDa 
• Atom Count: 3922 
• Modelled Residue Count: 447 
• Deposited Residue Count: 460 
• Unique protein chains: 1

1EKE

CRYSTAL STRUCTURE OF CLASS II RIBONUCLEASE H (RNASE HII) WITH MES LIGAND

• PDB DOI: 10.2210/pdb1EKE/pdb

• Classification: HYDROLASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2000-03-07 Released: 2000-09-13 
• Deposition Author(s): Lai, L.H., Yokota, H., Hung, L.W., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 

Literature

Crystal structure of archaeal RNase HII: a homologue of human major RNase H

Lai, L., Yokota, H., Hung, L.W., Kim, R., Kim, S.H.

(2000) Structure 8: 897-904

• PubMed: 10997908 
• DOI: 10.1016/s0969-2126(00)00179-9
• Primary Citation of Related Structures:  
  1EKE


• PubMed Abstract: 
  

RNases H are present in all organisms and cleave RNAs in RNA/DNA hybrids. There are two major types of RNases H that have little similarity in sequence, size and specificity. The structure of RNase HI, the smaller enzyme and most abundant in bacteria, has been extensively studied. However, no structural information is available for the larger RNase H, which is most abundant in eukaryotes and archaea. Mammalian RNase H participates in DNA replication, removal of the Okazaki fragments and possibly DNA repair.

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Organizational Affiliation: 

Department of Chemistry, University of California, Berkeley 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RIBONUCLEASE HII	A, B	230	Methanocaldococcus jannaschii	Mutation(s): 3  EC: 3.1.26.4
UniProt
Find proteins for Q57599 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q57599  Go to UniProtKB:  Q57599

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], D [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.262 
• R-Value Work: 0.210 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.484	α = 90
b = 55.424	β = 111.85
c = 72.145	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2000-03-07 
• Released Date: 2000-09-13 
Deposition Author(s): Lai, L.H., Yokota, H., Hung, L.W., Kim, R., Kim, S.H., Berkeley Structural Genomics Center (BSGC)

Revision History  

• Version 1.0: 2000-09-13
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance