1S96 | pdb_00001s96

The 2.0 A X-ray structure of Guanylate Kinase from E.coli

• PDB DOI: https://doi.org/10.2210/pdb1S96/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-02-03 Released: 2004-02-10 
• Deposition Author(s): Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Vincent, J., Rodrigues, K., Lesley, S.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.247 (Depositor) 
• R-Value Work: 
  0.195 (Depositor) 

Literature

The Structure of Guanylate Kinase from Escherichia coli at 2.0 A resolution

Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Vincent, J., Rodrigues, K., Lesley, S.A.

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 2  

Global Symmetry: Dihedral - D3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 51.02 kDa 
• Atom Count: 3,611 
• Modeled Residue Count: 409 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B	219	Escherichia coli	Mutation(s): 6  Gene Names: GMK, SPOR, B3648, C4473, SF3688, S4081 EC: 2.7.4.8
UniProt
Find proteins for P60546 (Escherichia coli (strain K12)) Explore P60546  Go to UniProtKB:  P60546

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], E [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
UNX	D [auth A]	UNKNOWN ATOM OR ION X

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: 2.00 Å
• R-Value Free:  0.247 (Depositor) 
• R-Value Work:  0.195 (Depositor) 

Space Group: P 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.552	α = 90
b = 124.552	β = 90
c = 124.552	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-02-10 
Deposition Author(s): Kreusch, A., Spraggon, G., Klock, H.E., McMullan, D., Vincent, J., Rodrigues, K., Lesley, S.A.

Revision History  

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Structure summary