3PAF | pdb_00003paf

M. jannaschii L7Ae mutant

• PDB DOI: https://doi.org/10.2210/pdb3PAF/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2010-10-19 Released: 2011-11-02 
• Deposition Author(s): Biswas, S., Maxwell, E.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Structure and stability of M.jannaschii L7Ae El9 KtoQ mutant

Biswas, S., Gagnon, K.T., Mattos, C., Brown, B.A., Maxwell, E.S.

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)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 25.77 kDa 
• Atom Count: 1,998 
• Modeled Residue Count: 234 
• Deposited Residue Count: 234 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7Ae	A, B	117	Methanocaldococcus jannaschii	Mutation(s): 5  Gene Names: rpl7ae, MJ1203
UniProt
Find proteins for P54066 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore P54066  Go to UniProtKB:  P54066

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth B], F [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.183 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.443	α = 90
b = 55.634	β = 90
c = 103.039	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-11-02 
Deposition Author(s): Biswas, S., Maxwell, E.S.

Revision History  

• Version 1.0: 2011-11-02
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description