2DOO | pdb_00002doo

The structure of IMP-1 complexed with the detecting reagent (DansylC4SH) by a fluorescent probe

• PDB DOI: https://doi.org/10.2210/pdb2DOO/pdb

• Classification: HYDROLASE
• Organism(s): Serratia marcescens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-01 Released: 2006-11-28 
• Deposition Author(s): Kurosaki, H., Yamaguchi, Y., Yasuzawa, H., Jin, W., Yamagata, Y., Arakawa, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free: 
  0.225 (Depositor) 
• R-Value Work: 
  0.185 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Probing, inhibition, and crystallographic characterization of metallo-beta-lactamase (IMP-1) with fluorescent agents containing dansyl and thiol groups

Kurosaki, H., Yamaguchi, Y., Yasuzawa, H., Jin, W., Yamagata, Y., Arakawa, Y.

(2006) ChemMedChem 1: 969-972

• PubMed: 16937423 
• DOI: https://doi.org/10.1002/cmdc.200600115
• Primary Citation of Related Structures:  
  2DOO

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Organizational Affiliation: 

Department of Structure-function Physical Chemistry, Graduate School of Pharmaceutical Sciences, Kumamoto University Oe-honmachi 5-1, Kumamoto, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 51.37 kDa 
• Atom Count: 3,773 
• Modelled Residue Count: 432 
• Deposited Residue Count: 456 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BETA-LACTAMASE IMP-1	A, B	228	Serratia marcescens	Mutation(s): 0  Gene Names: BLAIMP-1 EC: 3.5.2.6 (PDB Primary Data), 3.1.26 (UniProt)
UniProt
Find proteins for P52699 (Serratia marcescens) Explore P52699  Go to UniProtKB:  P52699

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C4H	E [auth A], H [auth B]	N-[4-({[5-(DIMETHYLAMINO)-1-NAPHTHYL]SULFONYL}AMINO)BUTYL]-3-SULFANYLPROPANAMIDE C19 H27 N3 O3 S2 XPCVYJATJSZGJU-UHFFFAOYSA-N
ZN	C [auth A], D [auth A], F [auth B], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.43 Å
• R-Value Free:  0.225 (Depositor) 
• R-Value Work:  0.185 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.517	α = 90
b = 88.416	β = 90
c = 115.064	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-28 
Deposition Author(s): Kurosaki, H., Yamaguchi, Y., Yasuzawa, H., Jin, W., Yamagata, Y., Arakawa, Y.

Revision History  

• Version 1.0: 2006-11-28
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references, Derived calculations