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- PDB-2dhb: THREE DIMENSIONAL FOURIER SYNTHESIS OF HORSE DEOXYHAEMOGLOBIN AT ... -

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Basic information

Entry
Database: PDB / ID: 2dhb
TitleTHREE DIMENSIONAL FOURIER SYNTHESIS OF HORSE DEOXYHAEMOGLOBIN AT 2.8 ANGSTROMS RESOLUTION
Components
  • HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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 alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 2.8 Å
AuthorsPerutz, M.F.
Citation
Journal: Nature / Year: 1970
Title: Three dimensional fourier synthesis of horse deoxyhaemoglobin at 2.8 Angstrom units resolution.
Authors: Bolton, W. / Perutz, M.F.
History
DepositionNov 1, 1973Processing site: BNL
SupersessionJun 7, 1977ID: 1DHB
Revision 1.0Jun 7, 1977Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 29, 2014Group: Derived calculations
Revision 1.4Apr 4, 2018Group: Data collection / Other / Structure summary / Category: audit_author / pdbx_database_status
Item: _audit_author.name / _pdbx_database_status.process_site
Revision 1.5Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 285THE ENTRY COORDINATES ARE NOT PRESENTED IN THE STANDARD CRYSTAL FRAME.

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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)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3754
Polymers31,1432
Non-polymers1,2332
Water362
1
A: HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN (DEOXY) (BETA CHAIN)
hetero molecules

A: HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7518
Polymers62,2854
Non-polymers2,4664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)76.960, 81.700, 92.630
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Atom site foot note1: PERSONAL COMMUNICATION FROM M. F. PERUTZ (18-NOV-75) INDICATES THAT RESIDUE LEU B 112 SHOULD BE VAL B 112 AND RESIDUE VAL B 114 SHOULD BE LEU B 114.
2: REFERENCE 2 ABOVE INDICATES THAT RESIDUE ALA A 63 SHOULD BE GLY A 63 AND RESIDUE GLY A 65 SHOULD BE ALA A 65.

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Components

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


Mass: 15138.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P01958
#2: Protein HEMOGLOBIN (DEOXY) (BETA CHAIN)


Mass: 16004.222 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsPERSONAL COMMUNICATION FROM M. F. PERUTZ (18-NOV-75) INDICATES THAT RESIDUE LEU B 112 SHOULD BE VAL ...PERSONAL COMMUNICATION FROM M. F. PERUTZ (18-NOV-75) INDICATES THAT RESIDUE LEU B 112 SHOULD BE VAL B 112 AND RESIDUE VAL B 114 SHOULD BE LEU B 114. REFERENCE 2 ABOVE INDICATES THAT RESIDUE ALA A 63 SHOULD BE GLY A 63 AND RESIDUE GLY A 65 SHOULD BE ALA A 65.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.37 %
Crystal grow
*PLUS
Method: other

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Processing

RefinementHighest resolution: 2.8 Å
Details: IN THE COORDINATE FRAME OF THIS DATA-BANK ENTRY THE MOLECULAR DIAD IS ALIGNED WITH THE Y AXIS. TO GENERATE COORDINATES FOR THE ALPHA-2 AND BETA-2 CHAINS FROM THE ALPHA-1 AND BETA-1 ...Details: IN THE COORDINATE FRAME OF THIS DATA-BANK ENTRY THE MOLECULAR DIAD IS ALIGNED WITH THE Y AXIS. TO GENERATE COORDINATES FOR THE ALPHA-2 AND BETA-2 CHAINS FROM THE ALPHA-1 AND BETA-1 COORDINATES GIVEN HERE APPLY THE MTRIX TRANSFORMATION GIVEN BELOW.
Refinement stepCycle: LAST / Highest resolution: 2.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2201 0 86 2 2289

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