3LD3 | pdb_00003ld3

Crystal structure of inorganic phosphatase from anaplasma phagocytophilum at 1.75a resolution

• PDB DOI: https://doi.org/10.2210/pdb3LD3/pdb

• Classification: HYDROLASE
• Organism(s): Anaplasma phagocytophilum str. HZ
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2010-01-12 Released: 2010-03-31 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.182 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.161 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of inorganic phosphatase from anaplasma phagocytophilum at 1.75a resolution

Seattle Structural Genomics Center for Infectious Disease (SSGCID), Abendroth, J., Davies, D., Staker, B.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 43.96 kDa 
• Atom Count: 2,939 
• Modeled Residue Count: 342 
• Deposited Residue Count: 398 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inorganic pyrophosphatase	A, B	199	Anaplasma phagocytophilum str. HZ	Mutation(s): 0  Gene Names: ppa, APH_1101 EC: 3.6.1.1
UniProt
Find proteins for Q2GJ02 (Anaplasma phagocytophilum (strain HZ)) Explore Q2GJ02  Go to UniProtKB:  Q2GJ02

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4	C [auth A], D [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.182 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.161 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M33LD3

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 135.38	α = 90
b = 135.38	β = 90
c = 135.38	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: 2010-03-31 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID), Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2010-03-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description