6MG6 | pdb_00006mg6

Crystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27

• PDB DOI: https://doi.org/10.2210/pdb6MG6/pdb

• Classification: HYDROLASE
• Organism(s): Helicobacter pylori G27
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2018-09-13 Released: 2018-09-26 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of carbon-nitrogen hydrolase from Helicobacter pylori G27

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 137.56 kDa 
• Atom Count: 9,537 
• Modeled Residue Count: 1,172 
• Deposited Residue Count: 1,200 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbon-nitrogen hydrolase	A, B, C, D	300	Helicobacter pylori G27	Mutation(s): 0  Gene Names: HPG27_713
UniProt
Find proteins for B5Z7B9 (Helicobacter pylori (strain G27)) Explore B5Z7B9  Go to UniProtKB:  B5Z7B9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m36mg6

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 137.58	α = 90
b = 91.38	β = 90
c = 95.04	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
PARROT	phasing
Coot	model building
ARP/wARP	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-26 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2018-09-26
  Type: Initial release
  
• Version 1.1: 2024-03-13
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2024-04-03
  Changes: Refinement description