4L21 | pdb_00004l21

Crystal structure of Cimex nitrophorin F64V mutant ferrous NO complex

• PDB DOI: https://doi.org/10.2210/pdb4L21/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Cimex lectularius
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2013-06-04 Released: 2014-06-04 
• Deposition Author(s): Badgandi, H.B., Weichsel, A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Proximal Cysteine Protonation in Cimex Nitrophorin is key to efficient NO transport and release.

Badgandi, H.B., Hazzard, J.T., Weichsel, A., Tollin, G., Montfort, W.R.

To be published.

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: 32.23 kDa 
• Atom Count: 2,524 
• Modeled Residue Count: 280 
• Deposited Residue Count: 280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Salivary nitrophorin	A	280	Cimex lectularius	Mutation(s): 1
UniProt
Find proteins for O76745 (Cimex lectularius) Explore O76745  Go to UniProtKB:  O76745

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth A]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NO	C [auth A]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNC	A	L-PEPTIDE LINKING	C3 H6 N2 O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.219 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.182	α = 90
b = 41.68	β = 94.89
c = 65.457	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-06-04 
Deposition Author(s): Badgandi, H.B., Weichsel, A., Montfort, W.R.

Revision History  

• Version 1.0: 2014-06-04
  Type: Initial release
  
• Version 1.1: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary