7afv

Crystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand

Method: X-RAY DIFFRACTION Dmax: 60.6 Å Quality: EXCELLENT

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

Beta-2-microglobulin

Homo sapiens

UniProt P61769

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 × 4 PDB declaration: tetramer(4) Consistent with protein copy count Chain A; UniProt 27–116 Chain B; UniProt 27–116 Not recorded TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SJK 5-oxidanylidene-~{N}-(2-sulfanylethyl)-2,3-dihydro-[1,3]thiazolo[3,2-a]pyrimidine-6-carboxamide × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;Drop protein volume 0.2 uL Drop well volume 0.1 uL 0.04 M Porpheus Alcohol Mix (Complex ingredient) 0.1 M Morpheus Buffer System 3 pH 8.5 (Buffer) 31 %w/v Morpheus Precipitant Mix 4 (Precipitant) Stock Solutions: Porpheus Alcohol Mix 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M (RS)-1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol (for a final concentration of 6.7 mM of 1,6-hexanediol, 1-butanol, (RS)-1,2-propanediol, 2-propanol, 1,4-butanediol, 1,3-propanediol) Morpheus Buffer System 3 pH 8.5 1M Tris and 1M BICINE (for a final concentration of 39.1 mM Bicine pH = 5.03 and 60.9 M Tris pH = 10.83) Morpheus Precipitant Mix 25% w/v PEG 3350, 25% w/v PEG 1000, 25% v/v MPD (for a final concentration of 7.75% w/v PEG 1000, 7.75% w/v PEG 3350 and 7.75% v/v MPD) Resolution 2.40 Å R-free 0.288

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.

1313 other PDB entries and 1998 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B2MG_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–91; UniProt 27–116 Author chain B; PDBConstruct 2–91; UniProt 27–116

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 7afv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7afv
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7afv
Deposition date deposition_date2020-09-20
Structure title titleCrystal structure of tetrameric beta-2-microglobulin deltaN6 S52C stabilized by a covalent ligand
Keywords keywordsbeta-2-microglobulin, tetramer, covalent inhibitor, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.06
Radius of gyration Rg (electron density) rg_electron17.93
Forward intensity I(0) i08848720.00
Molecular weight molecular_weight21698.0 kDa
Excluded volume excluded_volume26979 ų
Envelope volume envelope_volume34083 ų
Hydration-shell volume shell_volume16164 ų
Envelope diameter envelope_diameter60.2
Shell Rg shell_rg23.55
Envelope Rg envelope_rg18.09
Shape Rg shape_rg17.94
Total Rg total_rg18.84
Total atoms total_atoms1528
Residues n_residues178
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 dmax60.6
Rg (real space) rg_real18.97
Rg uncertainty (real space) rg_real_error0.36
I(0) (real space) i0_real8.8490e+06
I(0) uncertainty (real space) i0_real_error1.1200e+05
Rg (reciprocal space) rg_reciprocal18.99
I(0) (reciprocal space) i0_reciprocal8849000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary21.0
Skewness Skewness skewness0.173
Kurtosis Kurtosis kurtosis-0.545
Angular range angular_range— – 0.4150 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2518000.0000
Real-space data points n_real_points73
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd7afva_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)
Domain ID domain_idd7afvb_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.2 — C1 set domains (antibody constant domain-like)

8. Citations (1)

9. Files and Curves (10)