6NZX | pdb_00006nzx

Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1)

• PDB DOI: https://doi.org/10.2210/pdb6NZX/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Hadesarchaea archaeon YNP_N21
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-02-14 Released: 2019-03-06 
• Deposition Author(s): Teakel, S.L., Marama, M.S., Aragao, D., Forwood, J.K., Cahill, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.223 (Depositor) 

Starting Model: experimental

Literature

Hadesarchaea YNP_N21 cytochrome b5 domain protein (KUO41884.1)

Teakel, S.L., Marama, M.S., Aragao, D., Forwood, J.K., Cahill, M.A.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 9.24 kDa 
• Atom Count: 663 
• Modeled Residue Count: 76 
• Deposited Residue Count: 78 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome B5	A	78	Hadesarchaea archaeon YNP_N21	Mutation(s): 0  Gene Names: APU95_03975

Small Molecules

Ligands 1 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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.261 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.223 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.17	α = 90
b = 72.17	β = 90
c = 22.81	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-03-06 
Deposition Author(s): Teakel, S.L., Marama, M.S., Aragao, D., Forwood, J.K., Cahill, M.A.

Revision History  

• Version 1.0: 2019-03-06
  Type: Initial release
  
• Version 1.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-30
  Changes: Structure summary