5MVJ | pdb_00005mvj

Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1

• PDB DOI: https://doi.org/10.2210/pdb5MVJ/pdb

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


• Deposited: 2017-01-16 Released: 2018-05-02 
• Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Starting Model: experimental

Literature

Structure of DC8E8 Fab at pH 6.5 crystallized in space-group P1

Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

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 2  

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

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

Biological Assembly 3  

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 192.34 kDa 
• Atom Count: 13,492 
• Modeled Residue Count: 1,741 
• Deposited Residue Count: 1,760 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody Fab heavy chain	A [auth H], C [auth A], E [auth C], G [auth E]	221	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody kappa chain	B [auth L], D [auth B], F [auth D], H [auth F]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	I [auth F]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A [auth H], C [auth A], E [auth C], G [auth E]	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.272 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.219 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.22	α = 92.32
b = 82.26	β = 95.47
c = 89.31	γ = 89.82

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-02 
Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

Revision History  

• Version 1.0: 2018-05-02
  Type: Initial release
  
• Version 2.0: 2020-03-11
  Changes: Polymer sequence
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary