3OZ9 | pdb_00003oz9

Crystal Structure of anti-gp41 Fab NC-1

• PDB DOI: https://doi.org/10.2210/pdb3OZ9/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2010-09-24 Released: 2010-10-06 
• Deposition Author(s): Stanfield, R.L., Calarese, D.A., Jiang, S., Wilson, I.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 
  0.233 (Depositor), 0.227 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of anti-gp41 Fab NC-1

Stanfield, R.L., Calarese, D.A., Jiang, S., Wilson, I.A.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content 

• Total Structure Weight: 47.06 kDa 
• Atom Count: 3,833 
• Modeled Residue Count: 430 
• Deposited Residue Count: 430 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab NC-1 kappa light chain	A [auth L]	211	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q52L95 (Mus musculus) Explore Q52L95  Go to UniProtKB:  Q52L95

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab NC-1 IgG2a heavy chain	B [auth H]	219	Mus musculus	Mutation(s): 0
UniProt
Find proteins for P01863 (Mus musculus) Explore P01863  Go to UniProtKB:  P01863

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth L], D [auth L], E [auth H], F [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.233 (Depositor), 0.227 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.373	α = 90
b = 61.539	β = 90
c = 154.373	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
AMoRE	phasing
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-10-06 
Deposition Author(s): Stanfield, R.L., Calarese, D.A., Jiang, S., Wilson, I.A.

Revision History  

• Version 1.0: 2010-10-06
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-06-28
  Changes: Database references, Source and taxonomy, Structure summary
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary