5VZ1 | pdb_00005vz1

Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of Ebola nucleoprotein (EBOV, TAFV, BDBV strains)

• PDB DOI: https://doi.org/10.2210/pdb5VZ1/pdb

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


• Deposited: 2017-05-26 Released: 2018-06-27 
• Deposition Author(s): Radwanska, M.J., Derewenda, U., Kossiakoff, A., Derewenda, Z.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.268 (Depositor), 0.269 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Apo Antibody fragment (Fab) raised against C-terminal domain of Ebola nucleoprotein (EBOV, TAFV, BDBV strains)

Radwanska, M.J., Derewenda, U., Kossiakoff, A., Derewenda, Z.S.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 97.39 kDa 
• Atom Count: 6,810 
• Modeled Residue Count: 827 
• Deposited Residue Count: 900 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Apo Antibody Fab Light Chain	A, C	215	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Apo Antibody Fab Heavy Chain	B, D	235	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.268 (Depositor), 0.269 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.222 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.621	α = 90
b = 74.621	β = 90
c = 323.695	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-3000	data collection
HKL-3000	data processing
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing
PHENIX	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-06-27 
Deposition Author(s): Radwanska, M.J., Derewenda, U., Kossiakoff, A., Derewenda, Z.S.

Revision History  

• Version 1.0: 2018-06-27
  Type: Initial release
  
• Version 1.1: 2023-10-04
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-23
  Changes: Structure summary