1j40

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

Method: X-RAY DIFFRACTION Dmax: 122.6 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) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, pH 6.6, SMALL TUBES, temperature 293K Resolution 1.45 Å R-free 0.197
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) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, pH 6.6, SMALL TUBES, temperature 293K Resolution 1.45 Å R-free 0.197

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) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, pH 6.6, SMALL TUBES, temperature 293K Resolution 1.45 Å R-free 0.197
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) HNI PROTOPORPHYRIN IX CONTAINING NI(II) × 2 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 CMO CARBON MONOXIDE × 2 2FU BUT-2-ENEDIAL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:SMALL TUBES;pH 6.6;293 K;PEG 4000, 50mM citrate-ammonium buffer, pH 6.6, SMALL TUBES, temperature 293K Resolution 1.45 Å R-free 0.197

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 1j40

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1j40
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1j40
Deposition date deposition_date2003-02-21
Structure title titleDirect observation of photolysis-induced tertiary structural changes in human haemoglobin; Crystal structure of alpha(Ni)-beta(Fe-CO) hemoglobin (laser unphotolysed)
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_guinier38.35
Radius of gyration Rg (electron density) rg_electron38.15
Forward intensity I(0) i0234264000.00
Molecular weight molecular_weight129200.0 kDa
Excluded volume excluded_volume163410 ų
Envelope volume envelope_volume207850 ų
Hydration-shell volume shell_volume45982 ų
Envelope diameter envelope_diameter123.8
Shell Rg shell_rg43.53
Envelope Rg envelope_rg37.48
Shape Rg shape_rg38.15
Total Rg total_rg38.47
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 dmax122.6
Rg (real space) rg_real38.54
Rg uncertainty (real space) rg_real_error0.98
I(0) (real space) i0_real2.3430e+08
I(0) uncertainty (real space) i0_real_error3.7520e+06
Rg (reciprocal space) rg_reciprocal38.43
I(0) (reciprocal space) i0_reciprocal234200000.0000
Solution quality estimate total_estimate0.8446
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary35.9
Skewness Skewness skewness0.365
Kurtosis Kurtosis kurtosis-0.723
Angular range angular_range— – 0.2050 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha71240000.0000
Real-space data points n_real_points42
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.800; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.943; Smooth: 0.634

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_idd1j40a_
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_idd1j40b_
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_idd1j40c_
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_idd1j40d_
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_idd1j40e_
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_idd1j40f_
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_idd1j40g_
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_idd1j40h_
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_id1j40A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40C00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40E00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40F00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40G00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1j40H00
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)