8I75

Crystal structure of decarboxylated osteocalcin at pH 2.0

• PDB DOI: https://doi.org/10.2210/pdb8I75/pdb

• Classification: STRUCTURAL PROTEIN
• Organism(s): Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2023-01-31 Released: 2024-01-31 
• Deposition Author(s): Yokoyama, T., Nabeshima, Y., Obita, T., Mizuguchi, M.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 

Literature

Crystal structures of decarboxylated osteocalcin and implications for the interaction with its receptor

Mizuguchi, M., Yokoyama, T., Otani, T., Kuribara, S., Nabeshima, Y., Obita, T., Hirata, M., Kawano, K.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 8.5 kDa 
• Atom Count: 577 
• Modelled Residue Count: 62 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Osteocalcin	A, B	38	Bos taurus	Mutation(s): 0  Gene Names: BGLAP
UniProt
Find proteins for P02820 (Bos taurus) Explore P02820  Go to UniProtKB:  P02820

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.33 Å
• R-Value Free: 0.230 
• R-Value Work: 0.185 
• R-Value Observed: 0.187 
• Space Group: P 4₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.237	α = 90
b = 42.237	β = 90
c = 36.872	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-01-31 
Deposition Author(s): Yokoyama, T., Nabeshima, Y., Obita, T., Mizuguchi, M.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2024-01-31
  Type: Initial release