7cue

Crystal structure of HID2 bound to human Hemoglobin

Method: X-RAY DIFFRACTION Dmax: 111.9 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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain A; UniProt 1–142 Chain C; UniProt 1–142 Not recorded Hemoglobin subunit beta × 2 (P68871) Amino acid ABC transporter substrate-binding protein × 3 (B0LFQ8) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293.15 K;23% PEG 3350 (w/v), 100mM ammonium sulfate, 100mM BIS-TRIS Resolution 2.75 Å R-free 0.259

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 1–142; UniProt 1–142 Author chain C; PDBConstruct 1–142; UniProt 1–142

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain B; UniProt 1–147 Chain D; UniProt 1–147 Not recorded Hemoglobin subunit alpha × 2 (P69905) Amino acid ABC transporter substrate-binding protein × 3 (B0LFQ8) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293.15 K;23% PEG 3350 (w/v), 100mM ammonium sulfate, 100mM BIS-TRIS Resolution 2.75 Å R-free 0.259

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 1–147; UniProt 1–147 Author chain D; PDBConstruct 1–147; UniProt 1–147

Amino acid ABC transporter substrate-binding protein

Streptococcus pyogenes

UniProt B0LFQ8

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 × 7 PDB declaration: heptameric(7) Consistent with protein copy count Chain E; UniProt 171–294 Chain F; UniProt 171–294 Chain H; UniProt 171–294 Fragment:HID2 domain Hemoglobin subunit alpha × 2 (P69905) Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 5.5;293.15 K;23% PEG 3350 (w/v), 100mM ammonium sulfate, 100mM BIS-TRIS Resolution 2.75 Å R-free 0.259

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.

3 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name B0LFQ8_STRPY
Isoform
PDB entities 3
Chains and sequence ranges Author chain E; PDBConstruct 1–124; UniProt 171–294 Author chain F; PDBConstruct 1–124; UniProt 171–294 Author chain H; PDBConstruct 1–124; UniProt 171–294

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 7cue

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id7cue
Deposition date deposition_date2020-08-22
Structure title titleCrystal structure of HID2 bound to human Hemoglobin
Keywords keywords;Hemoglobin, Staphylococcus aureus, Hemoglobin binding protein, protein-protein interaction, Shr, heme acquisition, METAL BINDING PROTEIN ;; METAL BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.46
Radius of gyration Rg (electron density) rg_electron31.85
Forward intensity I(0) i0149031000.00
Molecular weight molecular_weight100220.0 kDa
Excluded volume excluded_volume126590 ų
Envelope volume envelope_volume161630 ų
Hydration-shell volume shell_volume43228 ų
Envelope diameter envelope_diameter121.5
Shell Rg shell_rg37.83
Envelope Rg envelope_rg32.09
Shape Rg shape_rg31.82
Total Rg total_rg32.45
Total atoms total_atoms7071
Residues n_residues898
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 dmax111.9
Rg (real space) rg_real32.48
Rg uncertainty (real space) rg_real_error1.11
I(0) (real space) i0_real1.4900e+08
I(0) uncertainty (real space) i0_real_error2.6620e+06
Rg (reciprocal space) rg_reciprocal32.47
I(0) (reciprocal space) i0_reciprocal149000000.0000
Solution quality estimate total_estimate0.8681
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary41.1
Skewness Skewness skewness0.408
Kurtosis Kurtosis kurtosis-0.115
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha51420000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.778; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.966

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd7cuea_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd7cueb_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd7cuec_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins
Domain ID domain_idd7cued_
Class classa — All alpha proteins
Fold Fold folda.1 — Globin-like
Superfamily Superfamily superfamilya.1.1 — Globin-like
Family Family familya.1.1.2 — Globins

8. Citations (1)

9. Files and Curves (10)