5MX3 | pdb_00005mx3

Structure of DC8E8 Fab crystallized at pH 8.5

• PDB DOI: https://doi.org/10.2210/pdb5MX3/pdb
• Entry: 5MX3 supersedes: 4OZ4

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


• Deposited: 2017-01-20 Released: 2017-02-01 
• Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 
  0.256 (Depositor), 0.289 (DCC) 
• R-Value Work: 
  0.219 (Depositor) 
• R-Value Observed: 
  0.220 (Depositor) 

Starting Model: experimental

Literature

Structure of DC8E8 Fab crystallized at pH 8.5

Skrabana, R.

To be published.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 95.72 kDa 
• Atom Count: 6,680 
• Modeled Residue Count: 876 
• Deposited Residue Count: 876 
• 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]	220	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
antibody kappa chain	B [auth L], D [auth B]	218	Mus musculus	Mutation(s): 0

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free:  0.256 (Depositor), 0.289 (DCC) 
• R-Value Work:  0.219 (Depositor) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.11	α = 90
b = 111.03	β = 90.38
c = 95.86	γ = 90

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: 2017-02-01 
Deposition Author(s): Skrabana, R., Novak, M., Cehlar, O., Kontsekova, E.
• This entry supersedes: 4OZ4

Revision History  

• Version 1.0: 2017-02-01
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 2.0: 2020-03-11
  Changes: Advisory, Polymer sequence
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Refinement description
• Version 2.2: 2024-11-20
  Changes: Structure summary