7TBR | pdb_00007tbr

Crystal structure of the TPM domain from the Rhodothermus marinus protein Rhom172_1776

• PDB DOI: https://doi.org/10.2210/pdb7TBR/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Rhodothermus marinus SG0.5JP17-172
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2021-12-22 Released: 2023-01-25 
• Deposition Author(s): Pellizza, L., Klinke, S., Aran, M.
• Funding Organization(s): Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the TPM domain from the Rhodothermus marinus protein Rhom172_1776

Pellizza, L., Klinke, S., Aran, M.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 15.95 kDa 
• Atom Count: 1,260 
• Modeled Residue Count: 142 
• Deposited Residue Count: 145 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TPM_phosphatase domain-containing protein	A	145	Rhodothermus marinus SG0.5JP17-172	Mutation(s): 0  Gene Names: Rhom172_1776

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	B [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.78	α = 90
b = 37.56	β = 118.15
c = 48.53	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MxCuBE	data collection
XDS	data scaling
XDS	data reduction
MoRDa	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-01-25 
Deposition Author(s): Pellizza, L., Klinke, S., Aran, M.

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Funding Organization	Location	Grant Number
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2017-1873
Agencia Nacional de Promocion Cientifica y Tecnologica (FONCYT)	Argentina	PICT-2019-0033

Revision History  

• Version 1.0: 2023-01-25
  Type: Initial release
  
• Version 1.1: 2023-10-25
  Changes: Data collection, Refinement description