4BBO | pdb_00004bbo

Crystal structure of core-bradavidin

• PDB DOI: https://doi.org/10.2210/pdb4BBO/pdb

• Classification: BIOTIN-BINDING PROTEIN
• Organism(s): Bradyrhizobium japonicum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-27 Released: 2013-10-16 
• Deposition Author(s): Airenne, T.T., Johnson, M.S., Maatta, J.A.E., Hytonen, V.H., Kulomaa, M.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.179 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.148 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of Core-Bradavidin

Airenne, T.T., Maatta, J.A.E., Nordlund, H., Kulomaa, M.S., Johnson, M.S.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 50.45 kDa 
• Atom Count: 3,829 
• Modeled Residue Count: 448 
• Deposited Residue Count: 472 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BLR5658 PROTEIN	A, B, C, D	118	Bradyrhizobium japonicum	Mutation(s): 0
UniProt
Find proteins for Q89IH6 (Bradyrhizobium diazoefficiens (strain JCM 10833 / BCRC 13528 / IAM 13628 / NBRC 14792 / USDA 110)) Explore Q89IH6  Go to UniProtKB:  Q89IH6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BTN	E [auth A], G [auth B], I [auth C], K [auth D]	BIOTIN C10 H16 N2 O3 S YBJHBAHKTGYVGT-ZKWXMUAHSA-N
GOL	F [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ACT	H [auth B], J [auth C], L [auth D]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.179 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.148 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.946	α = 90
b = 78.647	β = 90
c = 100.12	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-10-16 
Deposition Author(s): Airenne, T.T., Johnson, M.S., Maatta, J.A.E., Hytonen, V.H., Kulomaa, M.S.

Revision History  

• Version 1.0: 2013-10-16
  Type: Initial release
  
• Version 1.1: 2018-01-17
  Changes: Data collection
• Version 1.2: 2019-05-08
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-10-23
  Changes: Structure summary