2KRJ

High-Resolution Solid-State NMR Structure of a 17.6 kDa Protein

• PDB DOI:  https://doi.org/10.2210/pdb2KRJ/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-12-18 Released: 2010-02-23 
• Deposition Author(s): Bertini, I., Bhaumik, A., De Pa pe, G., Griffin, R.G., Lelli, M., Lewandowski, J.R., Luchinat, C.

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Experimental Data Snapshot

• Method: SOLID-STATE NMR
• Conformers Calculated: 2000 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Literature

High-resolution solid-state NMR structure of a 17.6 kDa protein.

Bertini, I., Bhaumik, A., De Paepe, G., Griffin, R.G., Lelli, M., Lewandowski, J.R., Luchinat, C.

(2010) J Am Chem Soc 132: 1032-1040

• PubMed: 20041641 
• DOI: https://doi.org/10.1021/ja906426p
• Primary Citation of Related Structures:  
  2KRJ


• PubMed Abstract: 
  

The use of pseudocontact shifts arising from paramagnetic metal ions in a microcrystalline protein sample is proposed as a strategy to obtain unambiguous signal assignments in solid-state NMR spectra enabling distance extraction for protein structure calculation. With this strategy, 777 unambiguous (281 sequential, 217 medium-range, and 279 long-range) distance restraints could be obtained from PDSD, DARR, CHHC, and the recently introduced PAR and PAIN-CP solid-state experiments for the cobalt(II)-substituted catalytic domain of matrix metalloproteinase 12 (159 amino acids, 17.6 kDa). The obtained structure is a high resolution one, with backbone rmsd of 1.0 +/- 0.2 A, and is in good agreement with the X-ray structure (rmsd to X-ray 1.3 A). The proposed strategy, which may be generalized for nonmetalloproteins with the use of paramagnetic tags, represents a significant step ahead in protein structure determination using solid-state NMR.

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Organizational Affiliation: 

Magnetic Resonance Center, CERM, University of Florence, Via L. Sacconi, 6-50019 Sesto Fiorentino, Italy. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.82 kDa 
• Atom Count: 1,186 
• Modelled Residue Count: 152 
• Deposited Residue Count: 152 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage metalloelastase	A	152	Homo sapiens	Mutation(s): 0  Gene Names: MMP12, HME EC: 3.4.24.65
UniProt & NIH Common Fund Data Resources
Find proteins for P39900 (Homo sapiens) Explore P39900  Go to UniProtKB:  P39900
PHAROS:  P39900

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CO	B [auth A]	COBALT (II) ION Co XLJKHNWPARRRJB-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLID-STATE NMR
• Conformers Calculated: 2000 
• Conformers Submitted: 20 
• Selection Criteria: target function 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Bertini, I., Bhaumik, A., De Pa pe, G., Griffin, R.G., Lelli, M., Lewandowski, J.R., Luchinat, C.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2019-11-20
  Changes: Advisory, Data collection, Database references, Derived calculations, Experimental preparation