9bcj

Crystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae

Method: X-RAY DIFFRACTION Dmax: 93.0 Å Quality: GOOD

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

Hemoglobin subunit alpha

OrganismNot specified

UniProt P69905

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 2–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Membrane protein × 2 (Q6NEE5) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;20% PEG-2000 MME, 100 mM Tris, 240 mM TMAO Resolution 1.69 Å R-free 0.215

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.

348 other PDB entries and 412 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–141; UniProt 2–142

Hemoglobin subunit beta

OrganismNot specified

UniProt P68871

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain B; UniProt 2–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Membrane protein × 2 (Q6NEE5) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;20% PEG-2000 MME, 100 mM Tris, 240 mM TMAO Resolution 1.69 Å R-free 0.215

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.

343 other PDB entries and 399 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name HBB_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 1–146; UniProt 2–147

Membrane protein

Corynebacterium diphtheriae NCTC 13129

UniProt Q6NEE5

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 heterocomplex Heteromer Protein × 6 PDB declaration: hexameric(6) Consistent with protein copy count Chain C; UniProt 32–229 Not recorded Hemoglobin subunit alpha × 2 (P69905) Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 GOL GLYCEROL × 6 PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;298 K;20% PEG-2000 MME, 100 mM Tris, 240 mM TMAO Resolution 1.69 Å R-free 0.215

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.

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q6NEE5_CORDI
Isoform
PDB entities 3
Chains and sequence ranges Author chain C; PDBConstruct 1–198; UniProt 32–229

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 9bcj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9bcj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9bcj
Deposition date deposition_date2024-04-09
最后修订 last_revision2025-01-08
Structure title titleCrystal structure of human hemoglobin in complex with the HbpA receptor from Corynebacterium diphtheriae
Keywords keywordsComplex, Hemoglobin, heme, beta-sandwich, PROTEIN BINDING; PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier27.13
Radius of gyration Rg (electron density) rg_electron26.53
Forward intensity I(0) i043569700.00
Molecular weight molecular_weight52294.0 kDa
Excluded volume excluded_volume65808 ų
Envelope volume envelope_volume79419 ų
Hydration-shell volume shell_volume26237 ų
Envelope diameter envelope_diameter98.5
Shell Rg shell_rg32.35
Envelope Rg envelope_rg26.74
Shape Rg shape_rg26.52
Total Rg total_rg27.20
Total atoms total_atoms3691
Residues n_residues471
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 dmax93.0
Rg (real space) rg_real27.22
Rg uncertainty (real space) rg_real_error0.84
I(0) (real space) i0_real4.3570e+07
I(0) uncertainty (real space) i0_real_error6.6580e+05
Rg (reciprocal space) rg_reciprocal27.20
I(0) (reciprocal space) i0_reciprocal43570000.0000
Solution quality estimate total_estimate0.8748
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.3
Skewness Skewness skewness0.418
Kurtosis Kurtosis kurtosis-0.308
Angular range angular_range— – 0.2900 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha10520000.0000
Real-space data points n_real_points59
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.826; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.927; Smooth: 0.964

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

8. Citations (1)

9. Files and Curves (10)