3onz

Human tetrameric hemoglobin: proximal nitrite ligand at beta

Method: X-RAY DIFFRACTION Dmax: 64.5 Å Quality: REASONABLE

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 2–142 Fragment:Hemoglobin Chain A Hemoglobin subunit beta × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 NO2 NITRITE ION × 4 MBN TOLUENE × 8 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 7.1;295 K;sodium phospahte, potassium phosphate, toluene, nitrite, hemoglobin, pH 7.1, LIQUID DIFFUSION, temperature 295K Resolution 2.09 Å R-free 0.280

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 2–147 Fragment:Hemoglobin Chain B Hemoglobin subunit alpha × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 NO2 NITRITE ION × 4 MBN TOLUENE × 8 X-RAY DIFFRACTION X-ray crystallization conditions:LIQUID DIFFUSION;pH 7.1;295 K;sodium phospahte, potassium phosphate, toluene, nitrite, hemoglobin, pH 7.1, LIQUID DIFFUSION, temperature 295K Resolution 2.09 Å R-free 0.280

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

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 3onz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3onz
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3onz
Deposition date deposition_date2010-08-30
Structure title titleHuman tetrameric hemoglobin: proximal nitrite ligand at beta
Keywords keywordsnitrite, human hemoglobin, OXYGEN TRANSPORT; OXYGEN TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.98
Radius of gyration Rg (electron density) rg_electron18.69
Forward intensity I(0) i015387900.00
Molecular weight molecular_weight31029.0 kDa
Excluded volume excluded_volume39396 ų
Envelope volume envelope_volume44659 ų
Hydration-shell volume shell_volume19760 ų
Envelope diameter envelope_diameter59.5
Shell Rg shell_rg25.15
Envelope Rg envelope_rg18.89
Shape Rg shape_rg18.69
Total Rg total_rg19.65
Total atoms total_atoms2196
Residues n_residues274
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 dmax64.5
Rg (real space) rg_real19.87
Rg uncertainty (real space) rg_real_error0.34
I(0) (real space) i0_real1.5390e+07
I(0) uncertainty (real space) i0_real_error1.9720e+05
Rg (reciprocal space) rg_reciprocal19.89
I(0) (reciprocal space) i0_reciprocal15390000.0000
Solution quality estimate total_estimate0.6626
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary25.4
Skewness Skewness skewness0.154
Kurtosis Kurtosis kurtosis-0.506
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3436000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 0.338; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3onza_
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_idd3onzb_
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 (2 domains)

Domain ID domain_id3onzA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id3onzB00
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)