3LNC | pdb_00003lnc

Crystal structure of guanylate kinase from Anaplasma phagocytophilum

• PDB DOI: https://doi.org/10.2210/pdb3LNC/pdb

• Classification: TRANSFERASE
• Organism(s): Anaplasma phagocytophilum str. HZ
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-02-02 Released: 2010-02-16 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of guanylate kinase from Anaplasma phagocytophilum

Abendroth, J., Sankaran, B., Davies, D., Staker, B.

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)

Macromolecule Content 

• Total Structure Weight: 53.23 kDa 
• Atom Count: 3,098 
• Modeled Residue Count: 376 
• Deposited Residue Count: 462 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanylate kinase	A, B	231	Anaplasma phagocytophilum str. HZ	Mutation(s): 0  Gene Names: gmk, APH_0170 EC: 2.7.4.8
UniProt
Find proteins for Q2GLF7 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GLF7  Go to UniProtKB:  Q2GLF7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5GP	C [auth A], D [auth B]	GUANOSINE-5'-MONOPHOSPHATE C10 H14 N5 O8 P RQFCJASXJCIDSX-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.244 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LNC

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.53	α = 90
b = 76.58	β = 90
c = 103.66	γ = 90

Software Package:

Software Name	Purpose
BOS	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-16 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-02-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-01
  Changes: Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description