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3trp

Crystal structure of recombinant rabbit skeletal calsequestrin

Method: X-RAY DIFFRACTION Dmax: 75.0 Å Quality: EXCELLENT
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Calsequestrin-1

Oryctolagus cuniculus

UniProt P07221

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 29–381 Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 3 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CA CALCIUM ION × 6 NA SODIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.88 Å R-free 0.208
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 29–381 Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 6 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 12 NA SODIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions Resolution 1.88 Å R-free 0.208

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.

Other PDB Difference from Current Entry 3TRP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A8Y CRYSTAL STRUCTURE OF CALSEQUESTRIN FROM RABBIT SKELETAL MUSCLE SARCOPLASMIC RETICULUM AT 2.4 A RESOLUTION Deposited 1998-03-31 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–395（367 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；pH 6.5
Resolution 2.40 Å R-free 0.242
3TRQ Crystal structure of native rabbit skeletal calsequestrin Deposited 2011-09-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–381（353 aa）
Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 CA CALCIUM ION × 6 NA SODIUM ION × 3 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.76 Å R-free 0.213
3TRQ Crystal structure of native rabbit skeletal calsequestrin Deposited 2011-09-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–381（353 aa）
Not recorded MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 4 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 CA CALCIUM ION × 12 NA SODIUM ION × 6 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.76 Å R-free 0.213
3US3 Recombinant rabbit skeletal calsequestrin-MPD complex Deposited 2011-11-22 Different construct Different ligand/ion Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–395（367 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 6 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 CA CALCIUM ION × 8 NA SODIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.74 Å R-free 0.232
3V1W Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin Deposited 2011-12-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–395（367 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 2 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 CA CALCIUM ION × 4 NA SODIUM ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.91 Å R-free 0.222
3V1W Molecular Basis for Multiple Ligand Binding of Calsequestrin and Potential Inhibition by Caffeine and Gallocatecin Deposited 2011-12-10 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 29–395（367 aa）
Not recorded MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 2 CA CALCIUM ION × 8 NA SODIUM ION × 4 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.91 Å R-free 0.222

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

View Construct and Data Evidence
UniProt name CASQ1_RABIT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–353； UniProt 29–381

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 3trp

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3trp
Deposition date deposition_date2011-09-09
Structure title titleCrystal structure of recombinant rabbit skeletal calsequestrin
Keywords keywordsCalcium-binding protein; Calcium-binding protein
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier24.20 Å
Radius of gyration Rg (electron density) rg_electron22.85 Å
Forward intensity I(0) i027587400.00
Molecular weight molecular_weight41234.0 kDa
Excluded volume excluded_volume51859 ų
Envelope volume envelope_volume65366 ų
Hydration-shell volume shell_volume23938 ų
Envelope diameter envelope_diameter77.3 Å
Shell Rg shell_rg29.49 Å
Envelope Rg envelope_rg23.12 Å
Shape Rg shape_rg22.83 Å
Total Rg total_rg23.80 Å
Total atoms total_atoms2905
Residues n_residues353
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax75.0 Å
Rg (real space) rg_real24.09 Å
Rg uncertainty (real space) rg_real_error0.39 Å
I(0) (real space) i0_real2.7590e+07
I(0) uncertainty (real space) i0_real_error3.6980e+05
Rg (reciprocal space) rg_reciprocal24.12 Å
I(0) (reciprocal space) i0_reciprocal27590000.0000
Solution quality estimate total_estimate0.9095
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.0 Å
Skewness Skewness skewness0.136
Kurtosis Kurtosis kurtosis-0.628
Angular range angular_range— – 0.3300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha7331000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.941; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id3trpA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3trpA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
Domain ID domain_id3trpA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology30 — Glutaredoxin
Homologous superfamily homologous superfamily10 — Glutaredoxin
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8. Citations (1)

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9. Files and Curves (10)