3KAT | pdb_00003kat

Crystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E

• PDB DOI: https://doi.org/10.2210/pdb3KAT/pdb

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


• Deposited: 2009-10-19 Released: 2009-10-27 
• Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.260 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.202 (Depositor), 0.220 (DCC) 

Literature

Northeast Structural Genomics Consortium Target HR3486E

Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: light scattering

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 12.73 kDa 
• Atom Count: 707 
• Modeled Residue Count: 84 
• Deposited Residue Count: 107 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NACHT, LRR and PYD domains-containing protein 1	A	107	Homo sapiens	Mutation(s): 0  Gene Names: CARD7, DEFCAP, KIAA0926, NAC, NALP1, NLRP1 EC: 3.6.4 (UniProt), 3.4 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9C000 (Homo sapiens) Explore Q9C000  Go to UniProtKB:  Q9C000
PHAROS:  Q9C000 GTEx:  ENSG00000091592

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.260 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.202 (Depositor), 0.220 (DCC) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 40.708	α = 90
b = 40.708	β = 90
c = 160.413	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
SHELX	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-27 
Deposition Author(s): Forouhar, F., Abashidze, M., Seetharaman, J., Mao, M., Xiao, R., Ciccosanti, C., Shastry, R., Everett, J.K., Nair, R., Acton, T.B., Rost, B., Montelione, G.T., Tong, L., Hunt, J.F., Northeast Structural Genomics Consortium (NESG)

Revision History  

• Version 1.0: 2009-10-27
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-25
  Changes: Author supporting evidence
• Version 1.3: 2019-07-17
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Structure summary