1PEE | pdb_00001pee

Crystal Structure of Nitrophorin 2 complex with imidazole

• PDB DOI: https://doi.org/10.2210/pdb1PEE/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Rhodnius prolixus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2003-05-21 Released: 2004-06-01 
• Deposition Author(s): Weihsel, A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.240 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.188 (Depositor) 

Starting Model: experimental

Literature

Conformational change and heme ruffling in nitrophorin 2, a nitric oxide carrier from kissing bug.

Weihsel, A., Montfort, W.R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.77 kDa 
• Atom Count: 1,629 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin 2	A	180	Rhodnius prolixus	Mutation(s): 0
UniProt
Find proteins for Q26241 (Rhodnius prolixus) Explore Q26241  Go to UniProtKB:  Q26241

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
IMD	C [auth A]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.240 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.188 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.68	α = 90
b = 34.68	β = 90
c = 258.78	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Blu-Ice	data collection
d*TREK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-06-01 
Deposition Author(s): Weihsel, A., Montfort, W.R.

Revision History  

• Version 1.0: 2004-06-01
  Type: Initial release
  
• Version 1.1: 2008-04-29
  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: 2024-10-16
  Changes: Structure summary