3QFO | pdb_00003qfo

Crystal structure of Streptococcal asymmetric Ap4A hydrolase and phosphodiesterase Spr1479/SapH im complex with AMP

• PDB DOI: https://doi.org/10.2210/pdb3QFO/pdb

• Classification: HYDROLASE
• Organism(s): Streptococcus pneumoniae R6
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-22 Released: 2011-08-24 
• Deposition Author(s): Jiang, Y.L., Zhang, J.W., Yu, W.L., Cheng, W., Zhang, C.C., Zhou, C.Z., Chen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Structural and enzymatic characterization of a Streptococcal ATP/diadenosine polyphosphate and phosphodiester hydrolase Spr1479/SapH

Jiang, Y.L., Zhang, J.W., Yu, W.L., Cheng, W., Zhang, C.C., Frolet, C., Di-guilmi, A.-M., Vernet, T., Zhou, C.Z., Chen, Y.

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: 63.76 kDa 
• Atom Count: 4,391 
• Modeled Residue Count: 500 
• Deposited Residue Count: 540 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative uncharacterized protein	A, B	270	Streptococcus pneumoniae R6	Mutation(s): 0  Gene Names: spr1479
UniProt
Find proteins for Q8DNX4 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6)) Explore Q8DNX4  Go to UniProtKB:  Q8DNX4

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AMP	C [auth A], F [auth B]	ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N
FE	D [auth A], G [auth B]	FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N
MN	E [auth A], H [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.245 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.185 (Depositor), 0.182 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.654	α = 90
b = 74.94	β = 90
c = 149.13	γ = 90

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-08-24 
Deposition Author(s): Jiang, Y.L., Zhang, J.W., Yu, W.L., Cheng, W., Zhang, C.C., Zhou, C.Z., Chen, Y.

Revision History  

• Version 1.0: 2011-08-24
  Type: Initial release
  
• Version 1.1: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description