2zrt

Crystal structure of Zn2+-bound form of des3-23ALG-2

Method: X-RAY DIFFRACTION Dmax: 141.7 Å Quality: GOOD

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

Programmed cell death protein 6

Homo sapiens

UniProt O75340

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 24–191 Chain B; UniProt 24–191 Fragment:UNP residues 24-191 ZN ZINC ION × 9 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.221
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 24–191 Chain D; UniProt 24–191 Fragment:UNP residues 24-191 ZN ZINC ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.221
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 24–191 Chain F; UniProt 24–191 Fragment:UNP residues 24-191 ZN ZINC ION × 10 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.221
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 24–191 Chain H; UniProt 24–191 Fragment:UNP residues 24-191 ZN ZINC ION × 7 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6;293 K;100mM MES, 15% ethanol, 200mM zinc acetate, pH6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.30 Å R-free 0.221

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 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PDCD6_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–168; UniProt 24–191 Author chain B; PDBConstruct 1–168; UniProt 24–191 Author chain C; PDBConstruct 1–168; UniProt 24–191 Author chain D; PDBConstruct 1–168; UniProt 24–191 Author chain E; PDBConstruct 1–168; UniProt 24–191 Author chain F; PDBConstruct 1–168; UniProt 24–191 Author chain G; PDBConstruct 1–168; UniProt 24–191 Author chain H; PDBConstruct 1–168; UniProt 24–191

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 2zrt

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2zrt
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2zrt
Deposition date deposition_date2008-09-01
Structure title titleCrystal structure of Zn2+-bound form of des3-23ALG-2
Keywords keywordspenta-EF-hand protein, Calcium-binding protein, APOPTOSIS, Calcium, Endoplasmic reticulum, Membrane, Nucleus, Polymorphism; APOPTOSIS
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier45.33
Radius of gyration Rg (electron density) rg_electron44.59
Forward intensity I(0) i0390868000.00
Molecular weight molecular_weight157340.0 kDa
Excluded volume excluded_volume194030 ų
Envelope volume envelope_volume301770 ų
Hydration-shell volume shell_volume56715 ų
Envelope diameter envelope_diameter142.2
Shell Rg shell_rg50.15
Envelope Rg envelope_rg42.15
Shape Rg shape_rg44.51
Total Rg total_rg45.11
Total atoms total_atoms11004
Residues n_residues1314
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 dmax141.7
Rg (real space) rg_real45.17
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real3.9090e+08
I(0) uncertainty (real space) i0_real_error6.2040e+06
Rg (reciprocal space) rg_reciprocal45.33
I(0) (reciprocal space) i0_reciprocal390900000.0000
Solution quality estimate total_estimate0.8876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary72.8
Skewness Skewness skewness0.056
Kurtosis Kurtosis kurtosis-0.761
Angular range angular_range— – 0.1750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha42220000.0000
Real-space data points n_real_points36
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.918; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.785

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id2zrtA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology238 — Recoverin; domain 1
Homologous superfamily homologous superfamily10 — EF-hand
Domain ID domain_id2zrtH00
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)