1LKA | pdb_00001lka

Porcine Pancreatic Elastase/Ca-Complex

• PDB DOI: https://doi.org/10.2210/pdb1LKA/pdb

• Classification: HYDROLASE
• Organism(s): Sus scrofa
• Mutation(s): No 


• Deposited: 2002-04-24 Released: 2002-08-28 
• Deposition Author(s): Weiss, M.S., Panjikar, S., Nowak, E., Tucker, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.216 (Depositor), 0.205 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.162 (DCC) 

Starting Model: experimental

Literature

Metal binding to porcine pancreatic elastase: calcium or not calcium.

Weiss, M.S., Panjikar, S., Nowak, E., Tucker, P.A.

(2002) Acta Crystallogr D Biol Crystallogr 58: 1407-1412

• PubMed: 12198296 
• DOI: https://doi.org/10.1107/S0907444902010934
• Primary Citation Related Structures: 
  1LKA, 1LKB


• PubMed Abstract: 
  

  Porcine pancreatic elastase has been crystallized at slightly acidic pH under two similar but slightly different conditions. Diffraction data were collected at a wavelength of 1.5 A to a maximum resolution of 1.7 A. Both difference electron-density maps and anomalous difference electron-density maps suggest that in crystals grown from a sodium sulfate solution PPE binds Na(+) in its metal-binding site. In contrast, PPE binds Ca(2+) in crystals grown from a solution containing sodium citrate and calcium chloride. This observation is in contradiction to most PPE structures reported in the PDB. In addition to the metal-binding site, up to three other binding sites, which appear to be anion-binding sites, could be identified based on the observed anomalous intensity differences.

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Organizational Affiliation: 
• EMBL Hamburg Outstation, c/o DESY, Notkestrasse 85, D-22603 Hamburg, Germany. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 26.06 kDa 
• Atom Count: 2,147 
• Modeled Residue Count: 240 
• Deposited Residue Count: 240 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elastase 1	A	240	Sus scrofa	Mutation(s): 0  EC: 3.4.21.36
UniProt
Find proteins for P00772 (Sus scrofa) Explore P00772  Go to UniProtKB:  P00772

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACT	B [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	D [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	C [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.216 (Depositor), 0.205 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.162 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.14	α = 90
b = 58.11	β = 90
c = 74.28	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
TRUNCATE	data reduction
REFMAC	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-08-28 
Deposition Author(s): Weiss, M.S., Panjikar, S., Nowak, E., Tucker, P.A.

Revision History  

• Version 1.0: 2002-08-28
  Type: Initial release
  
• Version 1.1: 2008-04-28
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-10-30
  Changes: Structure summary