7RIN | pdb_00007rin

Apo PTP1B by Native S-SAD at Room Temperature

• PDB DOI: https://doi.org/10.2210/pdb7RIN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2021-07-20 Released: 2021-07-28 
• Deposition Author(s): Greisman, J.B., Dalton, K.M., Hekstra, D.R.
• Funding Organization(s): Other private, National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.154 (Depositor), 0.155 (DCC) 
• R-Value Work: 
  0.132 (Depositor), 0.139 (DCC) 
• R-Value Observed: 
  0.133 (Depositor) 

Literature

Native SAD phasing at room temperature.

Greisman, J.B., Dalton, K.M., Sheehan, C.J., Klureza, M.A., Kurinov, I., Hekstra, D.R.

(2022) Acta Crystallogr D Struct Biol 78: 986-996

• PubMed: 35916223 
• DOI: https://doi.org/10.1107/S2059798322006799
• Primary Citation Related Structures: 
  7L84, 7LVC, 7MM1, 7RIN


• PubMed Abstract: 
  

  Single-wavelength anomalous diffraction (SAD) is a routine method for overcoming the phase problem when solving macromolecular structures. This technique requires the accurate measurement of intensities to determine differences between Bijvoet pairs. Although SAD experiments are commonly conducted at cryogenic temperatures to mitigate the effects of radiation damage, such temperatures can alter the conformational ensemble of the protein and may impede the merging of data from multiple crystals due to non-uniform freezing. Here, a strategy is presented to obtain high-quality data from room-temperature, single-crystal experiments. To illustrate the strengths of this approach, native SAD phasing at 6.55 keV was used to solve four structures of three model systems at 295 K. The resulting data sets allow automatic phasing and model building, and reveal alternate conformations that reflect the structure of proteins at room temperature.

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Organizational Affiliation: 
• Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, Massachusetts, USA.
Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts, USA.
NE-CAT, Department of Chemistry and Chemical Biology, Cornell University, 9700 South Cass Avenue, Argonne, Illinois, USA.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 37.59 kDa 
• Atom Count: 3,024 
• Modeled Residue Count: 298 
• Deposited Residue Count: 321 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase non-receptor type 1	A	321	Homo sapiens	Mutation(s): 2  Gene Names: PTPN1, PTP1B EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P18031 (Homo sapiens) Explore P18031  Go to UniProtKB:  P18031
PHAROS:  P18031 GTEx:  ENSG00000196396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	B [auth A], C [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.154 (Depositor), 0.155 (DCC) 
• R-Value Work:  0.132 (Depositor), 0.139 (DCC) 
• R-Value Observed: 0.133 (Depositor) 

Diffraction Data: https://doi.org/10.15785/SBGRID/845

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.538	α = 90
b = 89.538	β = 90
c = 106.144	γ = 120

Software Package:

Software Name	Purpose
DIALS	data reduction
Aimless	data scaling
AutoSol	phasing
PHENIX	model building
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2021-07-28 
Deposition Author(s): Greisman, J.B., Dalton, K.M., Hekstra, D.R.

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Funding Organization	Location	Grant Number
Other private	United States	Searle Scholars Program (SSP-2018-3240)
Other private	United States	George W. Merck Fund in the New York Community Trust (338034)
National Science Foundation (NSF, United States)	United States	DGE1745303

Revision History  

• Version 1.0: 2021-07-28
  Type: Initial release
  
• Version 1.1: 2021-08-11
  Changes: Database references
• Version 1.2: 2022-08-03
  Changes: Database references
• Version 1.3: 2022-08-17
  Changes: Database references
• Version 1.4: 2024-05-22
  Changes: Data collection