7YC6 | pdb_00007yc6

Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase

• PDB DOI: https://doi.org/10.2210/pdb7YC6/pdb

• Classification: TRANSFERASE
• Organism(s): Methanocaldococcus jannaschii
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-06-30 Released: 2023-06-14 
• Deposition Author(s): Chandrashekarmath, A., Bellur, A.
• Funding Organization(s): Department of Biotechnology (DBT, India), Science and Engineering Research Board (SERB)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of D110P mutant of GATase subunit of Methanocaldococcus jannaschii GMP synthetase

Chandrashekarmath, A., Bellur, A., Balaram, H.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 21.43 kDa 
• Atom Count: 1,468 
• Modeled Residue Count: 183 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GMP synthase [glutamine-hydrolyzing] subunit A	A	188	Methanocaldococcus jannaschii	Mutation(s): 1  EC: 6.3.5.2
UniProt
Find proteins for Q58970 (Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440)) Explore Q58970  Go to UniProtKB:  Q58970

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.221 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.199 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.08	α = 90
b = 63.08	β = 90
c = 101.94	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-06-14 
Deposition Author(s): Chandrashekarmath, A., Bellur, A.

---

Funding Organization	Location	Grant Number
Department of Biotechnology (DBT, India)	India	--
Science and Engineering Research Board (SERB)	India	--

Revision History  

• Version 1.0: 2023-06-14
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description