5I47 | pdb_00005i47

Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745

• PDB DOI: https://doi.org/10.2210/pdb5I47/pdb

• Classification: BIOSYNTHETIC PROTEIN
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2016-02-11 Released: 2016-03-16 
• Deposition Author(s): Chang, C., Duke, N., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Crystal structure of RimK domain protein ATP-grasp from Sphaerobacter thermophilus DSM 20745

Chang, C., Duke, N., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 58.52 kDa 
• Atom Count: 3,921 
• Modeled Residue Count: 522 
• Deposited Residue Count: 554 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RimK domain protein ATP-grasp	A, B	277	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_0213
UniProt
Find proteins for D1C6B4 (Sphaerobacter thermophilus (strain ATCC 49802 / DSM 20745 / KCCM 41009 / NCIMB 13125 / S 6022)) Explore D1C6B4  Go to UniProtKB:  D1C6B4

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.239 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.641	α = 90
b = 64.819	β = 90
c = 160.075	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
HKL-3000	data reduction
HKL-3000	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-03-16 
Deposition Author(s): Chang, C., Duke, N., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM115586

Revision History  

• Version 1.0: 2016-03-16
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-11-20
  Changes: Data collection, Database references, Structure summary