5MUQ | pdb_00005muq

Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom

• PDB DOI: https://doi.org/10.2210/pdb5MUQ/pdb

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


• Deposited: 2017-01-13 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: 2.62 Å
• R-Value Free: 
  0.279 (Depositor) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.216 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom

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

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 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 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 96.19 kDa 
• Atom Count: 6,722 
• Modeled Residue Count: 878 
• Deposited Residue Count: 878 
• 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 light chain	B [auth L], D [auth B]	219	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IMD	F [auth L], H [auth B]	IMIDAZOLE C3 H5 N2 RAXXELZNTBOGNW-UHFFFAOYSA-O
ZN	E [auth L], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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: 2.62 Å
• R-Value Free:  0.279 (Depositor) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.216 (Depositor) 

Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 113.51	α = 90
b = 113.51	β = 90
c = 69.39	γ = 120

Software Package:

Software Name	Purpose
XSCALE	data scaling
XDS	data reduction
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 1.1: 2019-07-10
  Changes: Data collection
• Version 1.2: 2019-07-17
  Changes: Data collection
• Version 2.0: 2020-03-11
  Changes: Polymer sequence
• Version 2.1: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-06
  Changes: Structure summary