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- PDB-1hbs: REFINED CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S. I. RESTRAINED LEA... -

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Basic information

Entry
Database: PDB / ID: 1hbs
TitleREFINED CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S. I. RESTRAINED LEAST-SQUARES REFINEMENT AT 3.0-ANGSTROMS RESOLUTION
Components
  • HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN S (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / Heme signaling / Late endosomal microautophagy / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / response to hydrogen peroxide / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / membrane / metal ion binding / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 3 Å
AuthorsPadlan, E.A. / Love, W.E.
Citation
Journal: J.Biol.Chem. / Year: 1985
Title: Refined crystal structure of deoxyhemoglobin S. I. Restrained least-squares refinement at 3.0-A resolution.
Authors: Padlan, E.A. / Love, W.E.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: Refined Crystal Structure of Deoxyhemoglobin S. II. Molecular Interactions in the Crystal
Authors: Padlan, E.A. / Love, W.E.
#2: Journal: Inserm Symp. / Year: 1978
Title: Intermolecular Interactions in Crystals of Human Deoxy Hemoglobin A, C, F and S
Authors: Love, W.E. / Fitzgerald, P.M.D. / Hanson, J.C. / Royerjunior, W.E.
#3: Journal: MOLECULAR STRUCTURE AND BIOLOGICAL ACTIVITY / Year: 1976
Title: Crystal Structure of Sickle-Cell Deoxyhemoglobin
Authors: Wishner, B.C. / Hanson, J.C. / Ringle, W.M. / Love, W.E.
#4: Journal: J.Mol.Biol. / Year: 1975
Title: Crystal Structure of Sickle-Cell Deoxyhemoglobin at 5 Angstroms Resolution
Authors: Wishner, B.C. / Ward, K.B. / Lattman, E.E. / Love, W.E.
#5: Journal: Proceedings of the First National Symposium on Sickle Cell Disease
Year: 1975
Title: Crystals of Deoxy Sickle Cell Hemoglobin
Authors: Wishner, B.C. / Love, W.E.
History
DepositionJun 2, 1982Processing site: BNL
Revision 1.0Jul 29, 1982Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
D: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
E: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
F: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
G: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
H: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,97416
Polymers124,0428
Non-polymers4,9328
Water00
1
A: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
D: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4878
Polymers62,0214
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10960 Å2
ΔGint-105 kcal/mol
Surface area24350 Å2
MethodPISA
2
E: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
F: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
G: HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)
H: HEMOGLOBIN S (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4878
Polymers62,0214
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11460 Å2
ΔGint-101 kcal/mol
Surface area24480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.330, 185.660, 52.970
Angle α, β, γ (deg.)90.00, 92.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9997, -0.0211, 0.01274), (-0.02101, -0.99975, -0.00726), (0.01289, 0.00699, -0.99989)
Vector: -31.14513, 95.20869, 79.04881)
DetailsTHERE ARE TWO DEOXY HEMOGLOBIN TETRAMERS IN THE ASYMMETRIC UNIT. CHAINS A, B, C, D CONSTITUTE THE FIRST TETRAMER AND CHAINS E, F, G, H CONSTITUTE THE SECOND. THESE TETRAMERS ARE RELATED APPROXIMATELY BY A NON-CRYSTALLOGRAPHIC TWO-FOLD SCREW AXIS PARALLEL TO THE A-AXIS OF THE CRYSTAL. APPLYING THE TRANSFORMATION GIVEN IN THE *MTRIX* RECORDS BELOW TO THE SECOND TETRAMER WILL YIELD APPROXIMATE COORDINATES FOR THE FIRST TETRAMER.

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Components

#1: Protein
HEMOGLOBIN S (DEOXY) (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
HEMOGLOBIN S (DEOXY) (BETA CHAIN)


Mass: 15860.216 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.93 %
Crystal grow
*PLUS
Method: unknown / PH range low: 5 / PH range high: 4
Components of the solutions
*PLUS
Common name: PEG6000

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 3 Å / Lowest resolution: 10 Å / Num. obs: 22633 / Rmerge(I) obs: 0.382

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Processing

RefinementRfactor obs: 0.254 / Highest resolution: 3 Å
Refinement stepCycle: LAST / Highest resolution: 3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8760 0 344 0 9104
Refinement
*PLUS
Lowest resolution: 5 Å / Num. reflection obs: 17662
Solvent computation
*PLUS
Displacement parameters
*PLUS

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