3OFF | pdb_00003off

Structured Domain of Drosophila melanogaster Boca p65 2 2 Crystal form

• PDB DOI: https://doi.org/10.2210/pdb3OFF/pdb

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


• Deposited: 2010-08-14 Released: 2011-03-02 
• Deposition Author(s): Collins, M.N., Hendrickson, W.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Literature

Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta-Propeller Domains

Collins, M.N., Hendrickson, W.A.

(2011) Structure 

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 11.01 kDa 
• Atom Count: 784 
• Modeled Residue Count: 85 
• Deposited Residue Count: 90 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LDLR chaperone boca	A	90	Drosophila melanogaster	Mutation(s): 0  Gene Names: boca, CG30498
UniProt
Find proteins for Q8T9B6 (Drosophila melanogaster) Explore Q8T9B6  Go to UniProtKB:  Q8T9B6

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	E [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NA	F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.226 (Depositor), 0.234 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.198 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.284	α = 90
b = 62.284	β = 90
c = 89.675	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Collins, M.N., Hendrickson, W.A.

Revision History  

• Version 1.0: 2011-03-02
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary