2B33 | pdb_00002b33

CRYSTAL STRUCTURE OF A PUTATIVE ENDORIBONUCLEASE (TM0215) FROM THERMOTOGA MARITIMA MSB8 AT 2.30 A RESOLUTION

• PDB DOI: https://doi.org/10.2210/pdb2B33/pdb

• Classification: HYDROLASE
• Organism(s): Thermotoga maritima MSB8
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2005-09-19 Released: 2005-09-27 
• Deposition Author(s): Joint Center for Structural Genomics (JCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 

Starting Model: other

Literature

Crystal structure of Protein synthesis inhibitor, putative (tm0215) from THERMOTOGA MARITIMA at 2.30 A resolution

Joint Center for Structural Genomics (JCSG)

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 31.72 kDa 
• Atom Count: 2,030 
• Modeled Residue Count: 253 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protein synthesis inhibitor, putative	A, B	140	Thermotoga maritima MSB8	Mutation(s): 0  Gene Names: tm0215
UniProt
Find proteins for Q9WY58 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WY58  Go to UniProtKB:  Q9WY58

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
EDO	C [auth A], D [auth A], F [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA	E [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 

Diffraction Data: https://doi.org/10.18430/M32B33

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.28	α = 90
b = 53.28	β = 90
c = 228.41	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-09-27 
Deposition Author(s): Joint Center for Structural Genomics (JCSG)

Revision History  

• Version 1.0: 2005-09-27
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Derived calculations, Source and taxonomy, Version format compliance
• Version 1.3: 2023-01-25
  Changes: Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Data collection, Refinement description