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- PDB-2hhb: THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS... -

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Basic information

Entry
Database: PDB / ID: 2hhb
TitleTHE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION
Components
  • HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


: / haptoglobin binding / nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex ...: / haptoglobin binding / 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 / peroxidase activity / carbon dioxide transport / Late endosomal microautophagy / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / 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 / PHOSPHATE ION / Hemoglobin subunit alpha / Hemoglobin subunit beta / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.74 Å
AuthorsFermi, G. / Perutz, M.F.
Citation
Journal: J.Mol.Biol. / Year: 1984
Title: The crystal structure of human deoxyhaemoglobin at 1.74 A resolution
Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R.
#1: Journal: Nature / Year: 1982
Title: Stereochemistry of Iron in Deoxyhaemoglobin
Authors: Perutz, M.F. / Hasnain, S.S. / Duke, P.J. / Sessler, J.L. / Hahn, J.E.
#3: Journal: Annu.Rev.Biochem. / Year: 1979
Title: Regulation of Oxygen Affinity of Hemoglobin. Influence of Structure of the Globin on the Heme Iron
Authors: Perutz, M.F.
#4: Journal: J.Mol.Biol. / Year: 1976
Title: Three-Dimensional Fourier Synthesis of Human Deoxyhemoglobin at 2.5 Angstroms Resolution, I.X-Ray Analysis
Authors: Teneyck, L.F. / Arnone, A.
#5: Journal: J.Mol.Biol. / Year: 1975
Title: Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 2.5 Angstroms Resolution, Refinement of the Atomic Model
Authors: Fermi, G.
#6: Journal: Nature / Year: 1970
Title: Three-Dimensional Fourier Synthesis of Human Deoxyhaemoglobin at 3.5 Angstroms Resolution
Authors: Muirhead, H. / Greer, J.
#2: Journal: Haemoglobin and Myoglobin. Atlas of Molecular Structures in Biology
Year: 1981
Authors: Fermi, G. / Perutz, M.F.
#7: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
#8: Journal: Atlas of Protein Sequence and Structure (Data Section)
Year: 1972
History
DepositionMar 7, 1984Processing site: BNL
SupersessionJul 18, 1984ID: 1HHB
Revision 1.0Jul 18, 1984Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_rmsd_angle / pdbx_validate_rmsd_bond / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark
Revision 2.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
D: HEMOGLOBIN (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,73710
Polymers62,0814
Non-polymers2,6566
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11610 Å2
ΔGint-102 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.150, 83.590, 53.800
Angle α, β, γ (deg.)90.00, 99.34, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: PROBABLY PHOSPHATE GROUP.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.952899, 0.301963, -0.028045), (0.302014, 0.936202, -0.179824), (-0.028043, -0.179784, -0.983303)
Vector: 17.04968, 4.93604, 81.78229)

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P01922, UniProt: P69905*PLUS
#2: Protein HEMOGLOBIN (DEOXY) (BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02023, UniProt: P68871*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHREE SETS OF COORDINATES FOR HUMAN HEMOGLOBIN WERE DEPOSITED SIMULTANEOUSLY. 2HHB. REFINED BY THE ...THREE SETS OF COORDINATES FOR HUMAN HEMOGLOBIN WERE DEPOSITED SIMULTANEOUSLY. 2HHB. REFINED BY THE METHOD OF JACK AND LEVITT. THIS ENTRY PRESENTS THE BEST ESTIMATE OF THE COORDINATES. 3HHB. SYMMETRY AVERAGED ABOUT THE (NON-CRYSTALLOGRAPHIC) MOLECULAR AXIS AND THEN RE-REGULARIZED BY THE ENERGY REFINEMENT METHOD OF LEVITT. THIS ENTRY PRESENTS COORDINATES THAT ARE ADEQUATE FOR MOST PURPOSES, SUCH AS COMPARISON WITH OTHER STRUCTURES. 4HHB. UNRESTRAINED REFINEMENT. THIS ENTRY PRESENTS COORDINATES THAT ARE USEFUL FOR STATISTICAL STUDIES (E.G. PHI/PSI ANGLES) WHERE DATA UNBIASED BY RESTRAINTS IS REQUIRED.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal grow
*PLUS
pH: 6.5 / Method: batch method / Details: Perutz, M.F., (1968) J.Crystall Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Crystal-IDSol-IDChemical formula
14 M11(NH4)2SO4
22 M11(NH4)H2PO4
32 M11(NH4)HPO4

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Data collection

Reflection
*PLUS
Highest resolution: 1.74 Å / Lowest resolution: 20 Å / Num. all: 56287 / Num. obs: 54034 / Num. measured all: 292000 / Rmerge(I) obs: 0.067

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Processing

RefinementRfactor Rwork: 0.16 / Highest resolution: 1.74 Å
Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO DIAD WHICH ...Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM STANDARD FOR HEMOGLOBINS. THE Y AXIS IS THE (NON CRYSTALLOGRAPHIC) MOLECULAR DIAD AND THE X AXIS IS THE PSEUDO DIAD WHICH RELATES THE ALPHA-1 AND BETA-1 CHAINS. THE TRANSFORMATION GIVEN IN THE *MTRIX* RECORDS BELOW WILL GENERATE COORDINATES FOR THE *C* AND *D* CHAINS FROM THE *A* AND *B* CHAINS RESPECTIVELY.
Refinement stepCycle: LAST / Highest resolution: 1.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 174 221 4779
Refinement
*PLUS
Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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