6WCT | pdb_00006wct

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate

• PDB DOI: https://doi.org/10.2210/pdb6WCT/pdb

• Classification: TRANSFERASE
• Organism(s): Stenotrophomonas maltophilia K279a
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-03-31 Released: 2020-04-08 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of a guanylate kinase from Stenotrophomonas maltophilia K279a bound to guanosine-5'-monophosphate

Edwards, T.E., Abendroth, J., Horanyi, P.S., Lorimer, D.D.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.46 kDa 
• Atom Count: 6,519 
• Modeled Residue Count: 808 
• Deposited Residue Count: 916 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B, C, D	229	Stenotrophomonas maltophilia K279a	Mutation(s): 0  Gene Names: gmk, Smlt3842 EC: 2.7.4.8
UniProt
Find proteins for B2FT06 (Stenotrophomonas maltophilia (strain K279a)) Explore B2FT06  Go to UniProtKB:  B2FT06

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP (Subject of Investigation/LOI)	E [auth A], G [auth B], H [auth C], I [auth D]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N
PO4	F [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
EDO	J [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.229 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.66	α = 90
b = 101.42	β = 92.03
c = 70.02	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-04-08 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-04-08
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description