1yih

T-to-T(High) quaternary transitions in human hemoglobin: betaP100A oxy (2.2MM IHP, 20% PEG) (1 test set)

Method: X-RAY DIFFRACTION Dmax: 69.8 Å Quality: EXCELLENT

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 × 4 OXY OXYGEN MOLECULE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:batch;pH 7;298 K;10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.0, batch, temperature 298.0K Resolution 2.00 Å R-free 0.247

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 1–141 Author chain C; PDBConstruct 1–141; UniProt 1–141

Hemoglobin beta chain

Homo sapiens

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 Mutation:V1M, P100A Hemoglobin alpha chain × 2 (P69905) HEM PROTOPORPHYRIN IX CONTAINING FE × 4 OXY OXYGEN MOLECULE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:batch;pH 7;298 K;10% PEG 6000, 10 MM POTASSIUM PHOSPHATE, 100 MM POTASSIUM CHLORIDE, 3 MM SODIUM DITHIONITE, 10 MG/ML DEOXYHB, 1 ATM N2, pH 7.0, batch, temperature 298.0K Resolution 2.00 Å R-free 0.247

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 1–146 Author chain D; 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 1yih

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1yih
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id1yih
Deposition date deposition_date2005-01-11
Structure title titleT-to-T(High) quaternary transitions in human hemoglobin: betaP100A oxy (2.2MM IHP, 20% PEG) (1 test set)
Keywords keywordsHEMOGLOBIN MUTANT, GLOBIN, 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_guinier24.73
Radius of gyration Rg (electron density) rg_electron23.47
Forward intensity I(0) i063992100.00
Molecular weight molecular_weight64595.0 kDa
Excluded volume excluded_volume81585 ų
Envelope volume envelope_volume96029 ų
Hydration-shell volume shell_volume32768 ų
Envelope diameter envelope_diameter70.7
Shell Rg shell_rg31.56
Envelope Rg envelope_rg23.17
Shape Rg shape_rg23.47
Total Rg total_rg24.37
Total atoms total_atoms4562
Residues n_residues574
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 dmax69.8
Rg (real space) rg_real24.48
Rg uncertainty (real space) rg_real_error0.35
I(0) (real space) i0_real6.3990e+07
I(0) uncertainty (real space) i0_real_error8.4180e+05
Rg (reciprocal space) rg_reciprocal24.54
I(0) (reciprocal space) i0_reciprocal63990000.0000
Solution quality estimate total_estimate0.9127
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary67.6
Skewness Skewness skewness-0.000
Kurtosis Kurtosis kurtosis-0.573
Angular range angular_range— – 0.3200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14760000.0000
Real-space data points n_real_points64
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.971; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.967; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd1yiha_
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_idd1yihb1
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_idd1yihc_
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_idd1yihd_
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_id1yihA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1yihB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1yihC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology490 — Globin-like
Homologous superfamily homologous superfamily10 — Globins
Domain ID domain_id1yihD00
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)