3A1P | pdb_00003a1p

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

• PDB DOI: https://doi.org/10.2210/pdb3A1P/pdb

• Classification: RIBOSOMAL PROTEIN
• Organism(s): Thermus thermophilus HB8
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-04-21 Released: 2010-04-21 
• Deposition Author(s): Kaminishi, T., Takemoto, C., Tatsuguchi, A., Kawazoe, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.245 (Depositor), 0.239 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.191 (DCC) 

Starting Models: experimental

Literature

Structure of Ribosome maturation protein RimM and Ribosomal protein S19

Kaminishi, T., Takemoto, C., Tatsuguchi, A., Kawazoe, M., Shirouzu, M., Yokoyama, S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 57.4 kDa 
• Atom Count: 4,317 
• Modeled Residue Count: 492 
• Deposited Residue Count: 510 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ribosome maturation factor rimM	A, C	162	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rimM
UniProt
Find proteins for Q5SJH5 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SJH5  Go to UniProtKB:  Q5SJH5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	B, D	93	Thermus thermophilus HB8	Mutation(s): 0  Gene Names: rpsS
UniProt
Find proteins for Q5SHP2 (Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)) Explore Q5SHP2  Go to UniProtKB:  Q5SHP2

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	E [auth D]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.245 (Depositor), 0.239 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.191 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.397	α = 90
b = 67.491	β = 94.82
c = 62.002	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Kaminishi, T., Takemoto, C., Tatsuguchi, A., Kawazoe, M., Shirouzu, M., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-11
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Refinement description