3ESQ | pdb_00003esq

Crystal Structure of Calcium-bound D,D-heptose 1.7-bisphosphate phosphatase from E. Coli

• PDB DOI: https://doi.org/10.2210/pdb3ESQ/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-10-06 Released: 2008-10-14 
• Deposition Author(s): Sugiman-Marangos, S.N., Junop, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.258 (Depositor) 
• R-Value Work: 
  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of D,D-heptose 1.7-bisphosphate phosphatase from E. Coli.

Taylor, P., Sugiman-Marangos, S.N., Zhang, K., DeLeon, G., Wright, G.D., Junop, M.S.

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)

Macromolecule Content 

• Total Structure Weight: 23.6 kDa 
• Atom Count: 1,617 
• Modeled Residue Count: 182 
• Deposited Residue Count: 211 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D,D-heptose 1,7-bisphosphate phosphatase	A	211	Escherichia coli K-12	Mutation(s): 0  Gene Names: b0200, gmhB, JW0196, yaeD EC: 3.1.3 (PDB Primary Data), 3.1.3.82 (UniProt)
UniProt
Find proteins for P63228 (Escherichia coli (strain K12)) Explore P63228  Go to UniProtKB:  P63228

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	C [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.258 (Depositor) 
• R-Value Work:  0.200 (Depositor), 0.201 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.904	α = 90
b = 50.585	β = 90
c = 52.638	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHENIX	model building
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-14 
Deposition Author(s): Sugiman-Marangos, S.N., Junop, M.S.

Revision History  

• Version 1.0: 2008-10-14
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-04-11
  Changes: Other
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description