1RMY | pdb_00001rmy

Crystal structure of AphA class B acid phosphatase/phosphotransferase ternary complex with deoxycytosine and phosphate bound to the catalytic metal

• PDB DOI: https://doi.org/10.2210/pdb1RMY/pdb

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


• Deposited: 2003-11-28 Released: 2004-12-14 
• Deposition Author(s): Calderone, V., Forleo, C., Benvenuti, M., Rossolini, G.M., Thaller, M.C., Mangani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 
  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.156 (Depositor) 

Starting Model: experimental

Literature

Insights in the catalytic mechanism of AphA from Escherichia coli

Calderone, V., Forleo, C., Benvenuti, M., Rossolini, G.M., Thaller, M.C., Mangani, S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content 

• Total Structure Weight: 47.71 kDa 
• Atom Count: 4,112 
• Modeled Residue Count: 418 
• Deposited Residue Count: 424 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Class B acid phosphatase	A, B	212	Escherichia coli	Mutation(s): 0  Gene Names: APHA, NAPA, B4055, SF4149, S3580 EC: 3.1.3.2
UniProt
Find proteins for P0AE22 (Escherichia coli (strain K12)) Explore P0AE22  Go to UniProtKB:  P0AE22

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DCZ	D [auth A], G [auth B]	2'-DEOXYCYTIDINE C9 H13 N3 O4 CKTSBUTUHBMZGZ-SHYZEUOFSA-N
PO4	F [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
MG	C [auth A], E [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free:  0.194 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.153 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.156 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.882	α = 90
b = 66.393	β = 119.66
c = 90.018	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-12-14 
Deposition Author(s): Calderone, V., Forleo, C., Benvenuti, M., Rossolini, G.M., Thaller, M.C., Mangani, S.

Revision History  

• Version 1.0: 2004-12-14
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description