5X5X | pdb_00005x5x

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

• PDB DOI: https://doi.org/10.2210/pdb5X5X/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-18 Released: 2018-02-21 
• Deposition Author(s): Komatsu, M., Dong, J., Ueda, H., Arai, R.
• Funding Organization(s): Cooperative Research Program of Network Joint Research Center for Materials and Devices, Japan Society for the Promotion of Science

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219

Arai, R., Komatsu, M., Dong, J., Ueda, H.

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)

Macromolecule Content 

• Total Structure Weight: 52.71 kDa 
• Atom Count: 3,623 
• Modeled Residue Count: 433 
• Deposited Residue Count: 481 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fd chain of anti-osteocalcin antibody KTM219	A [auth H]	249	Mus musculus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
L chain of anti-osteocalcin antibody KTM219	B [auth L]	232	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PG4	G [auth H], H	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
PGE	K [auth L], L	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	C [auth H], D [auth H], E [auth H], F [auth H]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
FMT	I [auth H], J [auth H], M [auth L]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.224 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.8	α = 90
b = 71.472	β = 90
c = 96.882	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing
Coot	model building
REFMAC	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-02-21 
Deposition Author(s): Komatsu, M., Dong, J., Ueda, H., Arai, R.

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Funding Organization	Location	Grant Number
Cooperative Research Program of Network Joint Research Center for Materials and Devices	Japan	20161175
Japan Society for the Promotion of Science	Japan	JP15H04191
Japan Society for the Promotion of Science	Japan	JP24780097
Japan Society for the Promotion of Science	Japan	JP16H00761
Japan Society for the Promotion of Science	Japan	JP16K05841
Japan Society for the Promotion of Science	Japan	JP26420793
Japan Society for the Promotion of Science	Japan	JP24360336

Revision History  

• Version 1.0: 2018-02-21
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-20
  Changes: Structure summary