1j3y

Direct observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed)

Method: X-RAY DIFFRACTION Dmax: 121.1 Å Quality: GOOD

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

Hemoglobin alpha Chain

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 1–141 Chain C; UniProt 1–141 Not recorded Hemoglobin beta Chain × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 Resolution 1.55 Å R-free 0.205
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 1–141 Chain G; UniProt 1–141 Not recorded Hemoglobin beta Chain × 2 (P68871) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 Resolution 1.55 Å R-free 0.205

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 1
Chains and sequence ranges Author chain A; PDBConstruct 1–141; UniProt 1–141 Author chain C; PDBConstruct 1–141; UniProt 1–141 Author chain E; PDBConstruct 1–141; UniProt 1–141 Author chain G; PDBConstruct 1–141; UniProt 1–141

Hemoglobin beta Chain

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 1–146 Chain D; UniProt 1–146 Not recorded Hemoglobin alpha Chain × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 Resolution 1.55 Å R-free 0.205
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 1–146 Chain H; UniProt 1–146 Not recorded Hemoglobin alpha Chain × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, SMALL TUBES, temperature 293K, pH 6.60 Resolution 1.55 Å R-free 0.205

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 398 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 1–146 Author chain D; PDBConstruct 1–146; UniProt 1–146 Author chain F; PDBConstruct 1–146; UniProt 1–146 Author chain H; PDBConstruct 1–146; UniProt 1–146

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 1j3y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1j3y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1j3y
Deposition date deposition_date2003-02-21
Structure title titleDirect observation of photolysis-induced tertiary structural changes in human hemoglobin; Crystal structure of alpha(Fe)-beta(Ni) hemoglobin (laser photolysed)
Keywords keywords;Tertiary structure changes, Crystal photolysis, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, OXYGEN STORAGE-TRANSPORT COMPLEX ;; OXYGEN STORAGE/TRANSPORT
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier38.46
Radius of gyration Rg (electron density) rg_electron38.27
Forward intensity I(0) i0233948000.00
Molecular weight molecular_weight129200.0 kDa
Excluded volume excluded_volume163410 ų
Envelope volume envelope_volume208320 ų
Hydration-shell volume shell_volume45865 ų
Envelope diameter envelope_diameter124.6
Shell Rg shell_rg43.73
Envelope Rg envelope_rg37.65
Shape Rg shape_rg38.27
Total Rg total_rg38.59
Total atoms total_atoms9132
Residues n_residues1148
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 dmax121.1
Rg (real space) rg_real38.66
Rg uncertainty (real space) rg_real_error1.16
I(0) (real space) i0_real2.3390e+08
I(0) uncertainty (real space) i0_real_error3.8470e+06
Rg (reciprocal space) rg_reciprocal38.54
I(0) (reciprocal space) i0_reciprocal233900000.0000
Solution quality estimate total_estimate0.8260
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary35.5
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.727
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha74560000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.808; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.940; Smooth: 0.373

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1j3ya_
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_idd1j3yb_
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_idd1j3yc_
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_idd1j3yd_
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_idd1j3ye_
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_idd1j3yf_
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_idd1j3yg_
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_idd1j3yh_
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 (8 domains)

Domain ID domain_id1j3yA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yE00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yG00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j3yH00
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)