1SG9 | pdb_00001sg9

Crystal structure of Thermotoga maritima protein HEMK, an N5-glutamine methyltransferase

• PDB DOI: https://doi.org/10.2210/pdb1SG9/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Thermotoga maritima
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2004-02-23 Released: 2004-08-17 
• Deposition Author(s): Agarwal, R., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.261 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.235 (Depositor) 

Literature

A novel mode of dimerization via formation of a glutamate anhydride crosslink in a protein crystal structure.

Agarwal, R., Burley, S.K., Swaminathan, S.

(2008) Proteins 71: 1038-1041

• PubMed: 18247349 
• DOI: https://doi.org/10.1002/prot.21962
• Primary Citation Related Structures: 
  1SG9

---

Organizational Affiliation: 
• Biology Department, Brookhaven National Laboratory, Upton, New York 11973, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 96.59 kDa 
• Atom Count: 6,841 
• Modeled Residue Count: 822 
• Deposited Residue Count: 846 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
hemK protein	A, B, C	282	Thermotoga maritima	Mutation(s): 0  EC: 2.1.1.297
UniProt
Find proteins for Q9WYV8 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WYV8  Go to UniProtKB:  Q9WYV8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	D [auth A], F [auth B], H [auth C]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
GLN	E [auth A], G [auth B], I [auth C]	GLUTAMINE C5 H10 N2 O3 ZDXPYRJPNDTMRX-VKHMYHEASA-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:  0.235 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.235 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.025	α = 90
b = 188.332	β = 90
c = 207.684	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MARMAD	data reduction
ADSC	data collection
SCALEPACK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-17 
Deposition Author(s): Agarwal, R., Swaminathan, S., Burley, S.K., New York SGX Research Center for Structural Genomics (NYSGXRC)

Revision History  

• Version 1.0: 2004-08-17
  Type: Initial release
  
• Version 1.1: 2008-07-14
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-02-03
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references