2P1B

Crystal structure of human nucleophosmin-core

• PDB DOI: https://doi.org/10.2210/pdb2P1B/pdb

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


• Deposited: 2007-03-03 Released: 2007-03-27 
• Deposition Author(s): Lee, H.H., Kim, H.S., Kang, J.Y., Lee, B.I., Ha, J.Y., Yoon, H.J., Lim, S.O., Jung, G., Suh, S.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.232 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 

Starting Model: experimental

Literature

Crystal structure of human nucleophosmin-core reveals plasticity of the pentamer-pentamer interface

Lee, H.H., Kim, H.S., Kang, J.Y., Lee, B.I., Ha, J.Y., Yoon, H.J., Lim, S.O., Jung, G., Suh, S.W.

(2007) Proteins 69: 672-678

• PubMed: 17879352 
• DOI: https://doi.org/10.1002/prot.21504
• Primary Citation of Related Structures:  
  2P1B

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Organizational Affiliation: 

Department of Chemistry, College of Natural Sciences, Seoul National University, Seoul 151-747, Korea.

Biological Assembly 1  

Global Symmetry: Dihedral - D5  (Explore in 3D)
Global Stoichiometry: Homo 10-mer - A10 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 generated by PISA,PQS (software)

Biological Assembly 3  

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

Biological assembly 3 generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 135.44 kDa 
• Atom Count: 7,686 
• Modelled Residue Count: 1,000 
• Deposited Residue Count: 1,220 
• 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	122	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P06748 (Homo sapiens) Explore P06748  Go to UniProtKB:  P06748
PHAROS:  P06748 GTEx:  ENSG00000181163

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 0.232 
• R-Value Work: 0.213 
• R-Value Observed: 0.213 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 99.262	α = 90
b = 107.841	β = 90
c = 108.694	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Lee, H.H., Kim, H.S., Kang, J.Y., Lee, B.I., Ha, J.Y., Yoon, H.J., Lim, S.O., Jung, G., Suh, S.W.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2007-10-19
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description