7C9J | pdb_00007c9j

Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension)

• PDB DOI: https://doi.org/10.2210/pdb7C9J/pdb

• Classification: TRANSFERASE
• Organism(s): Geobacillus stearothermophilus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-06-06 Released: 2021-06-09 
• Deposition Author(s): Takita, T., Mikami, B., Lei, Y., Jing, Y., Yamada, A., Yasukawa, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.214 (Depositor), 0.219 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.194 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Transglutaminase from Geobacillus stearothermophilus (without C-terminal extension)

Takita, T., Mikami, B., Lei, Y., Jing, Y., Yamada, A., Yamada, A.

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: 29.63 kDa 
• Atom Count: 1,837 
• Modeled Residue Count: 207 
• Deposited Residue Count: 254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein-glutamine gamma-glutamyltransferase	A	254	Geobacillus stearothermophilus	Mutation(s): 0  Gene Names: D9548_14210 EC: 2.3.2.13
UniProt
Find proteins for A0A3L7D5Y5 (Geobacillus stearothermophilus) Explore A0A3L7D5Y5  Go to UniProtKB:  A0A3L7D5Y5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	G [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
EDO	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSD	A	L-PEPTIDE LINKING	C3 H7 N O4 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.214 (Depositor), 0.219 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.194 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.09	α = 90
b = 94.09	β = 90
c = 158.14	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
MOLREP	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-06-09 
Deposition Author(s): Takita, T., Mikami, B., Lei, Y., Jing, Y., Yamada, A., Yasukawa, K.

Revision History  

• Version 1.0: 2021-06-09
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary