7MYT | pdb_00007myt

Crystal Structure of HPV L1-directed B25.M05 Fab

• PDB DOI: https://doi.org/10.2210/pdb7MYT/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2021-05-21 Released: 2022-11-09 
• Deposition Author(s): Singh, S., Pancera, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work: 
  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.175 (Depositor) 

Starting Model: experimental

Literature

Structural Characterization of Immune Responses to HPV vaccination

Singh, S., Pancera, M., Rodarte, J., Carter, J.

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)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 110.41 kDa 
• Atom Count: 6,812 
• Modeled Residue Count: 872 
• Deposited Residue Count: 1,018 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
B25.M05 Fab Heavy Chain	A, C [auth H]	274	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
B25.M05 Fab Light Chain	B, D [auth L]	235	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.223 (Depositor), 0.225 (DCC) 
• R-Value Work:  0.173 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.175 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.949	α = 94.406
b = 64.475	β = 97.125
c = 72.792	γ = 93.311

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-11-09 
Deposition Author(s): Singh, S., Pancera, M.

Revision History  

• Version 1.0: 2022-11-09
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary