5K4M | pdb_00005k4m

Directed evolutionary changes in MBL super family - NDM-1 Round 10 crystal-3

• PDB DOI: https://doi.org/10.2210/pdb5K4M/pdb

• Classification: HYDROLASE
• Organism(s): Klebsiella pneumoniae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2016-05-20 Released: 2017-04-26 
• Deposition Author(s): Hong, N.-S., Jackson, C.J., Carr, P.D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 
  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.142 (Depositor), 0.155 (DCC) 
• R-Value Observed: 
  0.145 (Depositor) 

Starting Model: experimental

Literature

Enzyme evolvability is contingent on the initial sequence background

Baier, F., Hong, N.-S., Yang, G., Carr, P.D., Jackson, C., Tokuriki, N.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.82 kDa 
• Atom Count: 1,982 
• Modeled Residue Count: 228 
• Deposited Residue Count: 245 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Metallo-beta-lactamase type 2	A	245	Klebsiella pneumoniae	Mutation(s): 13  Gene Names: blaNDM-1 EC: 3.5.2.6
UniProt
Find proteins for C7C422 (Klebsiella pneumoniae) Explore C7C422  Go to UniProtKB:  C7C422

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SV7	G [auth A], I [auth A]	phenylphosphonic acid C6 H7 O3 P QLZHNIAADXEJJP-UHFFFAOYSA-N
NPO	H [auth A]	P-NITROPHENOL C6 H5 N O3 BTJIUGUIPKRLHP-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free:  0.208 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.142 (Depositor), 0.155 (DCC) 
• R-Value Observed: 0.145 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.82	α = 90
b = 138.16	β = 90
c = 78.2	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-04-26 
Deposition Author(s): Hong, N.-S., Jackson, C.J., Carr, P.D.

Revision History  

• Version 1.0: 2017-04-26
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description