3kat

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

Method: X-RAY DIFFRACTION Dmax: 42.6 Å Quality: GOOD

1. Protein Identity and Related Structures Protein Identity & Related Structures

NACHT, LRR and PYD domains-containing protein 1

Homo sapiens

UniProt Q9C000

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1371–1467 Fragment:CARD domain Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.10 Å R-free 0.260
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1371–1467 Fragment:CARD domain Non-standard monomer:Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;291 K;Protein solution: 100mM NaCl, 5mM DTT, 0.02% NaN3, 10mM Tris-HCl (pH 7.5) . Reservoir solution: 18% PEG3350 and 150 mM sodium formate., VAPOR DIFFUSION, HANGING DROP, temperature 291K Resolution 3.10 Å R-free 0.260

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NALP1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 11–107; UniProt 1371–1467

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3kat

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3kat
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3kat
Deposition date deposition_date2009-10-19
Structure title titleCrystal Structure of the CARD domain of the human NLRP1 protein, Northeast Structural Genomics Consortium Target HR3486E
Keywords keywords;Structural Genomics, PSI-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, NESG, Alternative splicing, ATP-binding, Cytoplasm, Leucine-rich repeat, Nucleotide-binding, Nucleus, Polymorphism, APOPTOSIS ;; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier13.63
Radius of gyration Rg (electron density) rg_electron12.05
Forward intensity I(0) i02228650.00
Molecular weight molecular_weight10131.0 kDa
Excluded volume excluded_volume12610 ų
Envelope volume envelope_volume13649 ų
Hydration-shell volume shell_volume9793 ų
Envelope diameter envelope_diameter42.2
Shell Rg shell_rg17.58
Envelope Rg envelope_rg12.32
Shape Rg shape_rg12.04
Total Rg total_rg13.37
Total atoms total_atoms707
Residues n_residues82
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax42.6
Rg (real space) rg_real13.54
Rg uncertainty (real space) rg_real_error0.22
I(0) (real space) i0_real2.2290e+06
I(0) uncertainty (real space) i0_real_error2.1580e+04
Rg (reciprocal space) rg_reciprocal13.54
I(0) (reciprocal space) i0_reciprocal2229000.0000
Solution quality estimate total_estimate0.8084
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.3
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.261
Angular range angular_range— – 0.5000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha476300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (1)

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id3katA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology533 — Death Domain, Fas
Homologous superfamily homologous superfamily10 — Death Domain, Fas

8. Citations (1)

9. Files and Curves (10)