6AUF | pdb_00006auf

Crystal structure of Metalo beta Lactamases MIM-1 from Novosphingobium pentaromativorans

• PDB DOI: https://doi.org/10.2210/pdb6AUF/pdb

• Classification: HYDROLASE
• Organism(s): Novosphingobium pentaromativorans US6-1
• Expression System: Escherichia coli 042
• Mutation(s): No 


• Deposited: 2017-08-31 Released: 2018-09-12 
• Deposition Author(s): Selleck, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Literature

Crystal structure of Metalo beta Lactamases MIM-1 from Novosphingobium pentaromativorans

Selleck, C.

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: 32.2 kDa 
• Atom Count: 2,147 
• Modeled Residue Count: 273 
• Deposited Residue Count: 300 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase-like protein	A [auth B]	300	Novosphingobium pentaromativorans US6-1	Mutation(s): 0  Gene Names: NSU_3853
UniProt
Find proteins for G6EHN2 (Novosphingobium pentaromativorans US6-1) Explore G6EHN2  Go to UniProtKB:  G6EHN2

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CIT	D [auth B]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	B, C [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.961	α = 90
b = 67.961	β = 90
c = 216.67	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-09-12 
Deposition Author(s): Selleck, C.

Revision History  

• Version 1.0: 2018-09-12
  Type: Initial release
  
• Version 1.1: 2024-10-30
  Changes: Data collection, Database references, Structure summary