5J8N | pdb_00005j8n

Exonuclease III homologue Mm3148 from Methanosarcina mazei

• PDB DOI: https://doi.org/10.2210/pdb5J8N/pdb

• Classification: HYDROLASE
• Organism(s): Methanosarcina mazei Go1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-04-08 Released: 2016-04-27 
• Deposition Author(s): Lakomek, K., Dickmanns, A., Ficner, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free: 
  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Structure of the archael ExoIII homologue Mm3148 at 1.4 Angstrom

Lakomek, K., Dickmanns, A., Ber, S., Fritz, H.-J., Ficner, R.

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: 30.04 kDa 
• Atom Count: 2,508 
• Modeled Residue Count: 258 
• Deposited Residue Count: 258 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Exodeoxyribonuclease III	A	258	Methanosarcina mazei Go1	Mutation(s): 3  Gene Names: MM_3148 EC: 3.1.11.2
UniProt
Find proteins for Q8PSD1 (Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)) Explore Q8PSD1  Go to UniProtKB:  Q8PSD1

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	C [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.44 Å
• R-Value Free:  0.171 (Depositor), 0.170 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.726	α = 90
b = 64.564	β = 90
c = 84.89	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
MOLREP	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Lakomek, K., Dickmanns, A., Ficner, R.

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2019-07-17
  Changes: Data collection
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description