6VTV | pdb_00006vtv

Crystal structure of PuuD gamma-glutamyl-gamma-aminobutyrate hydrolase from E. coli

• PDB DOI: https://doi.org/10.2210/pdb6VTV/pdb

• Classification: HYDROLASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-02-13 Released: 2020-02-26 
• Deposition Author(s): Stogios, P.J., EVDOKIMOVA, E., DI LEO, R., SAVCHENKO, A., JOACHIMIAK, A., SATCHELL, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free: 
  0.218 (Depositor) 
• R-Value Work: 
  0.173 (Depositor) 
• R-Value Observed: 
  0.176 (Depositor) 

Starting Model: experimental

Literature

PuuD gamma-glutamyl-gamma-aminobutyrate hydrolase

Stogios, P.J.

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: 57.18 kDa 
• Atom Count: 4,435 
• Modeled Residue Count: 501 
• Deposited Residue Count: 516 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD	A, B	258	Escherichia coli K-12	Mutation(s): 0  Gene Names: puuD, ycjL, b1298, JW1291 EC: 3.5.1.94
UniProt
Find proteins for P76038 (Escherichia coli (strain K12)) Explore P76038  Go to UniProtKB:  P76038

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN (Subject of Investigation/LOI)	C [auth A], D [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.06 Å
• R-Value Free:  0.218 (Depositor) 
• R-Value Work:  0.173 (Depositor) 
• R-Value Observed: 0.176 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.161	α = 90
b = 72.177	β = 90
c = 98.631	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Currently 6VTV does not have a validation slider image.

Entry History & Funding Information

Deposition Data

• Released Date: 2020-02-26 
Deposition Author(s): Stogios, P.J., EVDOKIMOVA, E., DI LEO, R., SAVCHENKO, A., JOACHIMIAK, A., SATCHELL, K.J.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	HHSN272201700060C

Revision History  

• Version 1.0: 2020-02-26
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description