5EHD | pdb_00005ehd

Crystal structure of human nucleophosmin-core in complex with cytochrome c

• PDB DOI: https://doi.org/10.2210/pdb5EHD/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-10-28 Released: 2016-11-09 
• Deposition Author(s): Bernardo-Garcia, N., Hermoso, J.A., Gonzalez-Arzola, K., Diaz-Moreno, I., De la Rosa, M.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free: 
  0.229 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human nucleophosmin-core in complex with cytochrome c

Bernardo-Garcia, N., Hermoso, J.A., Gonzalez-Arzola, K., Diaz-Moreno, I., De la Rosa, M.A.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 4 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 253.61 kDa 
• Atom Count: 16,452 
• Modelled Residue Count: 2,125 
• Deposited Residue Count: 2,320 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nucleophosmin	A, B, C, D, E, F, G, H, I, J, K [auth a], L [auth b], M [auth c], N [auth d], O [auth e], P [auth f], Q [auth g], R [auth h], S [auth i], T [auth j]	116	Homo sapiens	Mutation(s): 0  Gene Names: NPM1, NPM
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens) Explore P06748  Go to UniProtKB:  P06748
PHAROS:  P06748 GTEx:  ENSG00000181163

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	U [auth A], V [auth G], W [auth b], X [auth f]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.55 Å
• R-Value Free:  0.229 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.799	α = 90
b = 179.72	β = 94.32
c = 104.3	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-09 
Deposition Author(s): Bernardo-Garcia, N., Hermoso, J.A., Gonzalez-Arzola, K., Diaz-Moreno, I., De la Rosa, M.A.

Revision History  

• Version 1.0: 2016-11-09
  Type: Initial release
  
• Version 1.1: 2024-01-10
  Changes: Data collection, Database references, Refinement description