3RQZ

Crystal structure of metallophosphoesterase from Sphaerobacter thermophilus

• PDB DOI: https://doi.org/10.2210/pdb3RQZ/pdb

• Classification: HYDROLASE
• Organism(s): Sphaerobacter thermophilus DSM 20745
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-04-28 Released: 2011-05-18 
• Deposition Author(s): Chang, C., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.150 
• R-Value Work: 0.123 
• R-Value Observed: 0.125 

Literature

Crystal structure of metallophosphoesterase from Sphaerobacter thermophilus

Chang, C., Wu, R., Clancy, S., Joachimiak, A.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 83.26 kDa 
• Atom Count: 6,082 
• Modelled Residue Count: 727 
• Deposited Residue Count: 738 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallophosphoesterase	A, B, C	246	Sphaerobacter thermophilus DSM 20745	Mutation(s): 0  Gene Names: Sthe_1642
UniProt
Find proteins for D1C4A9 (Sphaerobacter thermophilus (strain DSM 20745 / S 6022)) Explore D1C4A9  Go to UniProtKB:  D1C4A9

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth B], G [auth B], H [auth C], I [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	J [auth C]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.150 
• R-Value Work: 0.123 
• R-Value Observed: 0.125 
• Space Group: P 3₂

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.838	α = 90
b = 72.838	β = 90
c = 123.006	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
MLPHARE	phasing
DM	phasing
SHELXD	phasing
RESOLVE	phasing
ARP/wARP	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-05-18 
Deposition Author(s): Chang, C., Wu, R., Clancy, S., Joachimiak, A., Midwest Center for Structural Genomics (MCSG)

Revision History  

• Version 1.0: 2011-05-18
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance