4B1A | pdb_00004b1a

Crystal structure of lysozyme with Keggin molecule

• PDB DOI: https://doi.org/10.2210/pdb4B1A/pdb

• Classification: HYDROLASE
• Organism(s): Gallus gallus
• Mutation(s): No 


• Deposited: 2012-07-09 Released: 2013-02-06 
• Deposition Author(s): Mukhopadhyay, A., Silva, T.S., Romao, M.J., Romao, C.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.267 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.219 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Characterization of a Versatile Organometallic Pro-Drug (Corm) for Experimental Co Based Therapeutics.

Seixas, J.D., Mukhopadhyay, A., Santos-Silva, T., Otterbein, L.E., Gallo, D.J., Rodrigues, S.S., Guerreiro, B.H., Goncalves, A.M., Penacho, N., Marques, A.R., Coelho, A.C., Reis, P.M., Romao, M.J., Romao, C.C.

(2013) Dalton Trans 42: 5985

• PubMed: 23223860 
• DOI: https://doi.org/10.1039/c2dt32174b
• Primary Citation Related Structures: 
  4B1A


• PubMed Abstract: 
  

  The complex fac-[Mo(CO)(3)(histidinate)]Na has been reported to be an effective CO-Releasing Molecule in vivo, eliciting therapeutic effects in several animal models of disease. The CO releasing profile of this complex in different settings both in vitro and in vivo reveals that the compound can readily liberate all of its three CO equivalents under biological conditions. The compound has low toxicity and cytotoxicity and is not hemolytic. CO release is accompanied by a decrease in arterial blood pressure following administration in vivo. We studied its behavior in solution and upon the interaction with proteins. Reactive oxygen species (ROS) generation upon exposure to air and polyoxomolybdate formation in soaks with lysozyme crystals were observed as processes ensuing from the decomposition of the complex and the release of CO.

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Organizational Affiliation: 
• Alfama Lda, Taguspark, núcleo central 267, 2740-122 Porto Salvo, Portugal.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.21 kDa 
• Atom Count: 1,110 
• Modeled Residue Count: 129 
• Deposited Residue Count: 129 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LYSOZYME C	A	129	Gallus gallus	Mutation(s): 0  EC: 3.2.1.17
UniProt
Find proteins for P00698 (Gallus gallus) Explore P00698  Go to UniProtKB:  P00698

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K3G	B [auth A]	Phosphomolybdate keggin Mo12 O40 P STLJVKBKUFJRJR-UHFFFAOYSA-B
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	C [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.267 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.219 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.96	α = 90
b = 77.96	β = 90
c = 36.41	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-02-06 
Deposition Author(s): Mukhopadhyay, A., Silva, T.S., Romao, M.J., Romao, C.C.

Revision History  

• Version 1.0: 2013-02-06
  Type: Initial release
  
• Version 1.1: 2013-04-17
  Changes: Database references
• Version 1.2: 2018-11-14
  Changes: Data collection, Derived calculations
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary