3s48

Human Alpha-Haemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus

Method: X-RAY DIFFRACTION Dmax: 114.0 Å Quality: GOOD

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

Iron-regulated surface determinant protein H

Staphylococcus aureus

UniProt Q6G8J7

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 86–229 Fragment:first NEAT domain Hemoglobin subunit alpha × 1 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2M sodium sulphate, 0.1M Bis Tris propane, 16%(w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.05 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 86–229 Fragment:first NEAT domain Hemoglobin subunit alpha × 1 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2M sodium sulphate, 0.1M Bis Tris propane, 16%(w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.05 Å R-free 0.268

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.

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

View Construct and Data Evidence
UniProt name ISDH_STAAS
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 21–164; UniProt 86–229 Author chain B; PDBConstruct 21–164; UniProt 86–229

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 2–142 Not recorded Iron-regulated surface determinant protein H × 1 (Q6G8J7) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2M sodium sulphate, 0.1M Bis Tris propane, 16%(w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.05 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 2–142 Not recorded Iron-regulated surface determinant protein H × 1 (Q6G8J7) HEM PROTOPORPHYRIN IX CONTAINING FE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;293 K;0.2M sodium sulphate, 0.1M Bis Tris propane, 16%(w/v) PEG 3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 3.05 Å R-free 0.268

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 411 assemblies. Open the comparison page and filter oligomeric states

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

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 3s48

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3s48
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3s48
Deposition date deposition_date2011-05-19
Structure title titleHuman Alpha-Haemoglobin Complexed with the First NEAT Domain of IsdH from Staphylococcus aureus
Keywords keywordshaemoglobin, NEAT domain, IsdH, protein-protein complex, host-pathogen interaction, OXYGEN TRANSPORT-PROTEIN BINDING complex; OXYGEN TRANSPORT/PROTEIN BINDING
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.20
Radius of gyration Rg (electron density) rg_electron31.17
Forward intensity I(0) i061563300.00
Molecular weight molecular_weight63343.0 kDa
Excluded volume excluded_volume79808 ų
Envelope volume envelope_volume104650 ų
Hydration-shell volume shell_volume30279 ų
Envelope diameter envelope_diameter121.1
Shell Rg shell_rg35.08
Envelope Rg envelope_rg31.59
Shape Rg shape_rg31.16
Total Rg total_rg31.55
Total atoms total_atoms4484
Residues n_residues562
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 dmax114.0
Rg (real space) rg_real31.55
Rg uncertainty (real space) rg_real_error1.39
I(0) (real space) i0_real6.1560e+07
I(0) uncertainty (real space) i0_real_error1.2100e+06
Rg (reciprocal space) rg_reciprocal31.41
I(0) (reciprocal space) i0_reciprocal61560000.0000
Solution quality estimate total_estimate0.7981
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.1
Skewness Skewness skewness0.613
Kurtosis Kurtosis kurtosis-0.074
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19850000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.629; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.536; Smooth: 0.948

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3s48a_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.28 — NEAT domain-like
Family Family familyb.1.28.1 — NEAT domain
Domain ID domain_idd3s48b_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.28 — NEAT domain-like
Family Family familyb.1.28.1 — NEAT domain
Domain ID domain_idd3s48c_
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_idd3s48d_
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

CATH v4.4 (4 domains)

Domain ID domain_id3s48A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id3s48B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1850
Domain ID domain_id3s48C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id3s48D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins

8. Citations (1)

9. Files and Curves (10)