4RRP

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16

• PDB DOI: https://doi.org/10.2210/pdb4RRP/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens, Saccharomyces cerevisiae AWRI796
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-11-06 Released: 2014-12-31 
• Deposition Author(s): Kuzin, A., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Oconnell, P.T., Maglaqui, M., Bailey, L., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS), Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.253 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 

Starting Model: experimental

Literature

Crystal Structure of the Fab complexed with antigen Asf1p, Northeast Structural Genomics Consortium (NESG) Target PdR16

Kuzin, A., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Oconnell, P.T., Maglaqui, M., Bailey, L., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 5 assigned by authors.

Biological Assembly 6  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 6 assigned by authors.

Macromolecule Content

• Total Structure Weight: 402.46 kDa 
• Atom Count: 27,161 
• Modelled Residue Count: 3,503 
• Deposited Residue Count: 3,684 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody, light chain	A, C [auth B], E [auth C], G [auth D], I [auth E], K [auth F]	216	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab antibody, heavy chain	B [auth G], D [auth H], F [auth I], H [auth J], J [auth K], L	238	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Antigen Asf1p	M, N, O, P, Q, R	160	Saccharomyces cerevisiae AWRI796	Mutation(s): 0  Gene Names: AWRI796_2536

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	S [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.79 Å
• R-Value Free: 0.253 
• R-Value Work: 0.183 
• R-Value Observed: 0.185 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.725	α = 90
b = 181.309	β = 90
c = 259.286	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
SCALEPACK	data scaling
BALBES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-31 
Deposition Author(s): Kuzin, A., Lew, S., Seetharaman, J., Mao, L., Xiao, R., Oconnell, P.T., Maglaqui, M., Bailey, L., Everett, J.K., Acton, T.B., Montelione, G.T., Hunt, J.F., Tong, L., Chaperone-Enabled Studies of Epigenetic Regulation Enzymes (CEBS), Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2014-12-31
  Type: Initial release
  
• Version 1.1: 2015-01-07
  Changes: Structure summary
• Version 1.2: 2015-01-14
  Changes: Derived calculations, Structure summary
• Version 1.3: 2015-02-25
  Changes: Structure summary
• Version 1.4: 2015-07-22
  Changes: Source and taxonomy
• Version 1.5: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description