1qxp

Crystal Structure of a mu-like calpain

Method: X-RAY DIFFRACTION Dmax: 132.1 Å Quality: GOOD

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

mu-like calpain

Bos taurus

UniProt P97571

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 60–647 Mutation:C105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;295 K;PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.80 Å R-free 0.311
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 60–647 Mutation:C105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;295 K;PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.80 Å R-free 0.311

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.

9 other PDB entries and 10 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAN1_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 50–637; UniProt 60–647 Author chain B; PDBConstruct 50–637; UniProt 60–647

mu-like calpain

Bos taurus

UniProt Q07009

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 1–49 Chain A; UniProt 636–700 Mutation:C105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;295 K;PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.80 Å R-free 0.311
2 Insufficient information Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 1–49 Chain B; UniProt 636–700 Mutation:C105S No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.25;295 K;PEG 6000,morpholino ethane sulfonic acid, sodium chloride, n-nonyl-beta-D-maltoside , pH 6.25, VAPOR DIFFUSION, HANGING DROP, temperature 295K Resolution 2.80 Å R-free 0.311

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAN2_RAT
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–49; UniProt 1–49 Author chain A; PDBConstruct 638–702; UniProt 636–700 Author chain B; PDBConstruct 1–49; UniProt 1–49 Author chain B; PDBConstruct 638–702; UniProt 636–700

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 1qxp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1qxp
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1qxp
Deposition date deposition_date2003-09-08
Structure title titleCrystal Structure of a mu-like calpain
Keywords keywordsm-calpain, mu-calpain, catalytic triad, Ca(2+) requirement, HYDROLASE CHIMERA; HYDROLASE CHIMERA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier40.34
Radius of gyration Rg (electron density) rg_electron39.72
Forward intensity I(0) i0447936000.00
Molecular weight molecular_weight170620.0 kDa
Excluded volume excluded_volume212290 ų
Envelope volume envelope_volume310050 ų
Hydration-shell volume shell_volume63989 ų
Envelope diameter envelope_diameter143.5
Shell Rg shell_rg46.21
Envelope Rg envelope_rg39.19
Shape Rg shape_rg39.71
Total Rg total_rg40.11
Total atoms total_atoms12056
Residues n_residues1571
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 dmax132.1
Rg (real space) rg_real40.23
Rg uncertainty (real space) rg_real_error0.85
I(0) (real space) i0_real4.4790e+08
I(0) uncertainty (real space) i0_real_error7.3960e+06
Rg (reciprocal space) rg_reciprocal40.34
I(0) (reciprocal space) i0_reciprocal448000000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.2
Skewness Skewness skewness0.219
Kurtosis Kurtosis kurtosis-0.345
Angular range angular_range— – 0.1950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha88180000.0000
Real-space data points n_real_points40
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.877; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.905

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1qxpa1
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.8 — Penta-EF-hand proteins
Domain ID domain_idd1qxpa2
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.8 — Penta-EF-hand proteins
Domain ID domain_idd1qxpa3
Class classb — All beta proteins
Fold Fold foldb.14 — Calpain large subunit, middle domain (domain III)
Superfamily Superfamily superfamilyb.14.1 — Calpain large subunit, middle domain (domain III)
Family Family familyb.14.1.1 — Calpain large subunit, middle domain (domain III)
Domain ID domain_idd1qxpa4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.3 — Calpain large subunit, catalytic domain (domain II)
Domain ID domain_idd1qxpb1
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.8 — Penta-EF-hand proteins
Domain ID domain_idd1qxpb2
Class classa — All alpha proteins
Fold Fold folda.39 — EF Hand-like
Superfamily Superfamily superfamilya.39.1 — EF-hand
Family Family familya.39.1.8 — Penta-EF-hand proteins
Domain ID domain_idd1qxpb3
Class classb — All beta proteins
Fold Fold foldb.14 — Calpain large subunit, middle domain (domain III)
Superfamily Superfamily superfamilyb.14.1 — Calpain large subunit, middle domain (domain III)
Family Family familyb.14.1.1 — Calpain large subunit, middle domain (domain III)
Domain ID domain_idd1qxpb4
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.3 — Cysteine proteinases
Superfamily Superfamily superfamilyd.3.1 — Cysteine proteinases
Family Family familyd.3.1.3 — Calpain large subunit, catalytic domain (domain II)

CATH v4.4 (8 domains)

Domain ID domain_id1qxpA02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1qxpA03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily380
Domain ID domain_id1qxpA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1qxpA05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1qxpB02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology70 — Cathepsin B; Chain A
Homologous superfamily homologous superfamily10 — Cysteine proteinases
Domain ID domain_id1qxpB03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily380
Domain ID domain_id1qxpB04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id1qxpB05
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand

8. Citations (1)

9. Files and Curves (10)