5DR5 | pdb_00005dr5

Crystal structure of the sclerostin-neutralizing Fab AbD09097

• PDB DOI: https://doi.org/10.2210/pdb5DR5/pdb

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


• Deposited: 2015-09-15 Released: 2016-08-31 
• Deposition Author(s): Mueller, T.D., Boschert, V., Weidauer, S.E., Muth, E.M., Knappik, A., Frisch, C.
• Funding Organization(s): German Research Foundation, European Union

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 
  0.244 (Depositor), 0.246 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Model: experimental

Literature

Generation and Affinity Maturation of Neutralizing Anti-Sclerostin Antibodies

Boschert, V., Frisch, C., Back, J.W., van Pee, K., Weidauer, S.E., Muth, E.-M., Schmieder, P., Beerbaum, M., Knappik, A., Timmerman, P., Mueller, T.D.

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)

Macromolecule Content 

• Total Structure Weight: 50.25 kDa 
• Atom Count: 3,651 
• Modeled Residue Count: 439 
• Deposited Residue Count: 463 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
AbD09097 Fab heavy chain	A [auth H]	248	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
AbD09097 Fab light chain	B [auth L]	215	Homo sapiens	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free:  0.244 (Depositor), 0.246 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.193	α = 90
b = 78.495	β = 95.71
c = 59.196	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-31 
Deposition Author(s): Mueller, T.D., Boschert, V., Weidauer, S.E., Muth, E.M., Knappik, A., Frisch, C.

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Funding Organization	Location	Grant Number
German Research Foundation	Germany	DFG MU1095/5-1
European Union		TALOS, HEALTH-F2-2008-201099

Revision History  

• Version 1.0: 2016-08-31
  Type: Initial release
  
• Version 1.1: 2017-09-06
  Changes: Author supporting evidence
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-11-13
  Changes: Structure summary