1T6D | pdb_00001t6d

MIRAS phasing of the Aquifex aeolicus Ppx/GppA phosphatase: crystal structure of the type II variant

• PDB DOI: https://doi.org/10.2210/pdb1T6D/pdb

• Classification: HYDROLASE
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2004-05-06 Released: 2004-08-03 
• Deposition Author(s): Kristensen, O., Laurberg, M., Liljas, A., Kastrup, J.S., Gajhede, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.255 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.206 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.206 (Depositor) 

Literature

Structural characterization of the stringent response related exopolyphosphatase/guanosine pentaphosphate phosphohydrolase protein family

Kristensen, O., Laurberg, M., Liljas, A., Kastrup, J.S., Gajhede, M.

(2004) Biochemistry 43: 8894-8900

• PubMed: 15248747 
• DOI: https://doi.org/10.1021/bi049083c
• Primary Citation Related Structures: 
  1T6C, 1T6D


• PubMed Abstract: 
  

  Exopolyphosphatase/guanosine pentaphosphate phosphohydrolase (PPX/GPPA) enzymes play central roles in the bacterial stringent response induced by starvation. The high-resolution crystal structure of the putative Aquifex aeolicus PPX/GPPA phosphatase from the actin-like ATPase domain superfamily has been determined, providing the first insights to features of the common catalytic core of the PPX/GPPA family. The protein has a two-domain structure with an active site located in the interdomain cleft. Two crystal forms were investigated (type I and II) at resolutions of 1.53 and 2.15 A, respectively. This revealed a structural flexibility that has previously been described as a "butterfly-like" cleft opening around the active site in other actin-like superfamily proteins. A calcium ion is observed at the center of this region in type I crystals, substantiating that PPX/GPPA enzymes use metal ions for catalysis. Structural analysis suggests that nucleotides bind at a similar position to that seen in other members of the superfamily.

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Organizational Affiliation: 
• Biostructural Research, Department of Medicinal Chemistry, The Danish University of Pharmaceutical Sciences, Universitetsparken 2, DK-2100 Copenhagen, Denmark. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 72.45 kDa 
• Atom Count: 5,194 
• Modeled Residue Count: 603 
• Deposited Residue Count: 630 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
exopolyphosphatase	A, B	315	Aquifex aeolicus VF5	Mutation(s): 5  Gene Names: ppx EC: 3.6.1.11 (PDB Primary Data), 3.6.1.40 (PDB Primary Data)
UniProt
Find proteins for O67040 (Aquifex aeolicus (strain VF5)) Explore O67040  Go to UniProtKB:  O67040

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	D [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
CL	C [auth A], E [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSX	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.255 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.206 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.206 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.461	α = 90
b = 83.565	β = 97.39
c = 69.764	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing
SHARP	phasing
ARP/wARP	model building
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-08-03 
Deposition Author(s): Kristensen, O., Laurberg, M., Liljas, A., Kastrup, J.S., Gajhede, M.

Revision History  

• Version 1.0: 2004-08-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Source and taxonomy, Version format compliance
• Version 1.3: 2021-11-10
  Changes: Database references, Derived calculations