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1bkr

CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM RESOLUTION

Method: X-RAY DIFFRACTION Dmax: 44.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

SPECTRIN BETA CHAIN

Homo sapiens

UniProt Q01082

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 172–280 Fragment：F-ACTIN BINDING DOMAIN RESIDUES 173 - 281 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 0.2 M SODIUM ACETATE 0.1 M SODIUM CACODYLATE PH 6.6 PEG8K 30% (W/V) Resolution 1.10 Å R-free 0.187

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 1BKR Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AA2 CALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN Deposited 1997-01-21 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 173–280（108 aa） Fragment：F-ACTIN BINDING DOMAIN RESIDUES 173 - 281
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.6；PROTEIN WAS CRYSTALLIZED FROM 30% PEG 8000, 100 MM SODIUM CACODYLATE, PH 6.6
Resolution 2.00 Å R-free 0.210
3EDV Crystal Structure of Repeats 14-16 of Beta2-Spectrin Deposited 2008-09-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1697–2015（319 aa） Fragment：Spectrin repeats 14-16
Chain B 1697–2015（319 aa） Fragment：Spectrin repeats 14-16
Not recorded MG MAGNESIUM ION × 13 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.250
3EDV Crystal Structure of Repeats 14-16 of Beta2-Spectrin Deposited 2008-09-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1697–2015（319 aa） Fragment：Spectrin repeats 14-16
Not recorded MG MAGNESIUM ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.250
3EDV Crystal Structure of Repeats 14-16 of Beta2-Spectrin Deposited 2008-09-03 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1697–2015（319 aa） Fragment：Spectrin repeats 14-16
Not recorded MG MAGNESIUM ION × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.1M TrisHCl, 14% PEG4000, 0.3M Magnesium Chloride, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.95 Å R-free 0.250

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

View Construct and Data Evidence
UniProt name SPTB2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–109； UniProt 172–280

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 1bkr

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1bkr
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1bkr
Deposition date deposition_date1998-07-10
Structure title titleCALPONIN HOMOLOGY (CH) DOMAIN FROM HUMAN BETA-SPECTRIN AT 1.1 ANGSTROM RESOLUTION
Keywords keywordsFILAMENTOUS ACTIN-BINDING DOMAIN, CYTOSKELETON, ACTIN-BINDING; ACTIN-BINDING
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_guinier14.29 Å
Radius of gyration Rg (electron density) rg_electron12.78 Å
Forward intensity I(0) i03148800.00
Molecular weight molecular_weight12550.0 kDa
Excluded volume excluded_volume15786 ų
Envelope volume envelope_volume17117 ų
Hydration-shell volume shell_volume11302 ų
Envelope diameter envelope_diameter44.1 Å
Shell Rg shell_rg18.67 Å
Envelope Rg envelope_rg13.10 Å
Shape Rg shape_rg12.73 Å
Total Rg total_rg14.27 Å
Total atoms total_atoms887
Residues n_residues108
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 dmax44.5 Å
Rg (real space) rg_real14.18 Å
Rg uncertainty (real space) rg_real_error0.21 Å
I(0) (real space) i0_real3.1490e+06
I(0) uncertainty (real space) i0_real_error3.2300e+04
Rg (reciprocal space) rg_reciprocal14.19 Å
I(0) (reciprocal space) i0_reciprocal3149000.0000
Solution quality estimate total_estimate0.8831
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary19.2 Å
Skewness Skewness skewness0.041
Kurtosis Kurtosis kurtosis-0.371
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1012000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.838; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.984
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1bkra_
Class classa — All alpha proteins
Fold Fold folda.40 — CH domain-like
Superfamily Superfamily superfamilya.40.1 — Calponin-homology domain, CH-domain
Family Family familya.40.1.1 — Calponin-homology domain, CH-domain

CATH v4.4 (1 domains)

Domain ID domain_id1bkrA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology418 — Actin-binding Protein, T-fimbrin; domain 1
Homologous superfamily homologous superfamily10 — Calponin-like domain
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8. Citations (3)

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9. Files and Curves (10)