2D7T | pdb_00002d7t

Crystal structure of human anti polyhydroxybutyrate antibody Fv

• PDB DOI: https://doi.org/10.2210/pdb2D7T/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-11-29 Released: 2006-12-12 
• Deposition Author(s): Watanabe, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.214 (Depositor), 0.182 (DCC) 
• R-Value Work: 
  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.191 (Depositor) 

Starting Models: experimental

Literature

A human antibody fragment with high affinity for the biodegradable polymer film

Watanabe, H., Tsumoto, K., Taguchi, S., Yamashita, K., Doi, Y., Nishimiya, Y., Kondo, H., Umetsu, M., Kumagai, I.

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: 28.18 kDa 
• Atom Count: 1,907 
• Modeled Residue Count: 226 
• Deposited Residue Count: 255 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
anti polyhydroxybutyrate antibody Fv, heavy chain	A [auth H]	139	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q9UL95 (Homo sapiens) Explore Q9UL95  Go to UniProtKB:  Q9UL95

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
anti polyhydroxybutyrate antibody Fv, light chain	B [auth L]	116	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6GMX0 (Homo sapiens) Explore Q6GMX0  Go to UniProtKB:  Q6GMX0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.214 (Depositor), 0.182 (DCC) 
• R-Value Work:  0.190 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.191 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.409	α = 90
b = 73.62	β = 90
c = 103.299	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
CCP4	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-12 
Deposition Author(s): Watanabe, H.

Revision History  

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-10-25
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary