4NP1 | pdb_00004np1

NITROPHORIN 1 COMPLEX WITH NITRIC OXIDE

• PDB DOI: https://doi.org/10.2210/pdb4NP1/pdb

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


• Deposited: 1998-06-26 Released: 1998-11-11 
• Deposition Author(s): Weichsel, A., Andersen, J.F., Walker, F.A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.300 (Depositor), 0.276 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Nitric Oxide Binding to the Ferri-and Ferroheme States of Nitrophorin 1, a Reversible No-Binding Heme Protein from the Saliva of the Blood-Sucking Insect, Rhodnius Prolixus

Ding, X.D., Weichsel, A., Andersen, J.F., Shokhireva, T.Kh., Balfour, C., Pierik, A., Averill, B.A., Montfort, W.R., Walker, F.A.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 42.69 kDa 
• Atom Count: 3,127 
• Modeled Residue Count: 368 
• Deposited Residue Count: 368 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NITROPHORIN 1	A, B	184	Rhodnius prolixus	Mutation(s): 0
UniProt
Find proteins for Q26239 (Rhodnius prolixus) Explore Q26239  Go to UniProtKB:  Q26239

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], G [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
PO4	E [auth A], F [auth A], I [auth B], J [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO	D [auth A], H [auth B]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.300 (Depositor), 0.276 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.41	α = 90
b = 74.29	β = 99.19
c = 66.12	γ = 90

Software Package:

Software Name	Purpose
MADNES	data collection
AGROVATA/ROTAVATA	data reduction
X-PLOR	model building
X-PLOR	refinement
MADNES	data reduction
Agrovata	data scaling
ROTAVATA	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-11-11 
Deposition Author(s): Weichsel, A., Andersen, J.F., Walker, F.A., Montfort, W.R.

Revision History  

• Version 1.0: 1998-11-11
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-04-18
  Changes: Data collection, Other, Refinement description
• Version 1.4: 2023-08-09
  Changes: Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-23
  Changes: Data collection, Structure summary