4HIL | pdb_00004hil

1.25A Resolution Structure of Rat Type B Cytochrome b5

• PDB DOI: https://doi.org/10.2210/pdb4HIL/pdb

• Classification: ELECTRON TRANSPORT
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-10-11 Released: 2013-10-16 
• Deposition Author(s): Lovell, S., Battaile, K.P., Parthasarathy, S., Sun, N., Terzyan, S., Zhang, X., Rivera, M., Kuczera, K., Benson, D.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.152 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.138 (Depositor) 

Starting Model: experimental

Literature

1.25A Resolution Structure of Rat Type B Cytochrome b5

Parthasarathy, S., Sun, N., Lovell, S., Battaile, K.P., Terzyan, S., Zhang, X., Rivera, M., Kuczera, K., Benson, D.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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 21.03 kDa 
• Atom Count: 1,758 
• Modeled Residue Count: 166 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cytochrome b5 type B	A, B	87	Rattus norvegicus	Mutation(s): 0  Gene Names: Cyb5b, Cyb5m, Omb5
UniProt
Find proteins for P04166 (Rattus norvegicus) Explore P04166  Go to UniProtKB:  P04166

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
NA	E [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.152 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.137 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.138 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.609	α = 90
b = 67.847	β = 90
c = 70.342	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
MOLREP	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
JDirector	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Lovell, S., Battaile, K.P., Parthasarathy, S., Sun, N., Terzyan, S., Zhang, X., Rivera, M., Kuczera, K., Benson, D.R.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description