2AT8 | pdb_00002at8

0.96 A Crystal Structure Of Nitrophorin 4 From Rhodnius Prolixus Containing Fe(III) 2,4 Dimethyl Deuteroporphyrin IX Complexed With Nitric Oxide at pH 5.6

• PDB DOI: https://doi.org/10.2210/pdb2AT8/pdb

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


• Deposited: 2005-08-24 Released: 2006-08-22 
• Deposition Author(s): Amoia, A.M., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free: 
  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work: 
  0.165 (Depositor) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Heme distortion in nitrophorin 4: high resolution structures of mutated positions L123V and L133V and heme altered proteins

Amoia, A.M., 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: 21.01 kDa 
• Atom Count: 1,999 
• Modeled Residue Count: 184 
• Deposited Residue Count: 184 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin 4	A [auth X]	184	Rhodnius prolixus	Mutation(s): 0  EC: 1.7.6.1
UniProt
Find proteins for Q94734 (Rhodnius prolixus) Explore Q94734  Go to UniProtKB:  Q94734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FDD	C [auth X]	FE(III) 2,4-DIMETHYL DEUTEROPORPHYRIN IX C32 H32 Fe N4 O4 FALMRKXKKOZWNG-YDTHOXGASA-L
PO4	B [auth X]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
NO	D [auth X]	NITRIC OXIDE N O ODUCDPQEXGNKDN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.00 Å
• R-Value Free:  0.195 (Depositor), 0.189 (DCC) 
• R-Value Work:  0.165 (Depositor) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.211	α = 90
b = 42.582	β = 94.61
c = 52.935	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-22 
Deposition Author(s): Amoia, A.M., Montfort, W.R.

Revision History  

• Version 1.0: 2006-08-22
  Type: Initial release
  
• Version 1.1: 2008-01-31
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary