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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free:
0.221 (Depositor), 0.222 (DCC)
R-Value Work:
0.191 (Depositor), 0.193 (DCC)
R-Value Observed:
0.192 (Depositor)

Starting Model: experimental
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This is version 1.1 of the entry. See complete history.

Literature

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

Pellizza, L., Klinke, S., Aran, M.

To be published.

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

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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	3D Interactions
B3P Query on B3P Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.10 Å
R-Value Free: 0.221 (Depositor), 0.222 (DCC)
R-Value Work: 0.191 (Depositor), 0.193 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-01-25

Deposition Author(s):

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 (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.