7K3M | pdb_00007k3m

Crystal Structure of the Beta Lactamase Class D from Chitinophaga pinensis by Serial Crystallography

• PDB DOI: https://doi.org/10.2210/pdb7K3M/pdb

• Classification: HYDROLASE
• Organism(s): Chitinophaga pinensis DSM 2588
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-09-11 Released: 2020-09-23 
• Deposition Author(s): Kim, Y., Sherrell, D.A., Johnson, J., Lavens, A., Maltseva, N., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Fixed-target serial crystallography at the Structural Biology Center.

Sherrell, D.A., Lavens, A., Wilamowski, M., Kim, Y., Chard, R., Lazarski, K., Rosenbaum, G., Vescovi, R., Johnson, J.L., Akins, C., Chang, C., Michalska, K., Babnigg, G., Foster, I., Joachimiak, A.

(2022) J Synchrotron Radiat 29: 1141-1151

• PubMed: 36073872 
• DOI: https://doi.org/10.1107/S1600577522007895
• Primary Citation of Related Structures:  
  7K3M, 7L52


• PubMed Abstract: 
  

  Serial synchrotron crystallography enables the study of protein structures under physiological temperature and reduced radiation damage by collection of data from thousands of crystals. The Structural Biology Center at Sector 19 of the Advanced Photon Source has implemented a fixed-target approach with a new 3D-printed mesh-holder optimized for sample handling. The holder immobilizes a crystal suspension or droplet emulsion on a nylon mesh, trapping and sealing a near-monolayer of crystals in its mother liquor between two thin Mylar films. Data can be rapidly collected in scan mode and analyzed in near real-time using piezoelectric linear stages assembled in an XYZ arrangement, controlled with a graphical user interface and analyzed using a high-performance computing pipeline. Here, the system was applied to two β-lactamases: a class D serine β-lactamase from Chitinophaga pinensis DSM 2588 and L1 metallo-β-lactamase from Stenotrophomonas maltophilia K279a.

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Organizational Affiliation: 
• Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Center for Structural Genomics of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60667, USA.
Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA.
Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, USA.

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: 29.88 kDa 
• Atom Count: 2,160 
• Modeled Residue Count: 245 
• Deposited Residue Count: 250 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-lactamase	A	250	Chitinophaga pinensis DSM 2588	Mutation(s): 0  Gene Names: Cpin_0907 EC: 3.5.2.6

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
KCX	A	L-PEPTIDE LINKING	C7 H14 N2 O4		LYS
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.413	α = 90
b = 69.347	β = 90
c = 70.035	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
CRISpy	data collection
DIALS	data reduction
PRIME	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-09-23 
Deposition Author(s): Kim, Y., Sherrell, D.A., Johnson, J., Lavens, A., Maltseva, N., Endres, M., Babnigg, G., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2020-09-23
  Type: Initial release
  
• Version 1.1: 2020-10-28
  Changes: Refinement description
• Version 1.2: 2020-12-23
  Changes: Database references, Structure summary
• Version 1.3: 2024-04-03
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2026-03-25
  Changes: Database references, Structure summary