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- PDB-1hbh: STRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BE... -

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Basic information

Entry
Database: PDB / ID: 1hbh
TitleSTRUCTURE OF DEOXYHAEMOGLOBIN OF THE ANTARCTIC FISH PAGOTHENIA BERNACCHII AND STRUCTURAL BASIS OF THE ROOT EFFECT
Components
  • HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN (DEOXY) (BETA CHAIN)
KeywordsOXYGEN CARRIER
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / 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-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / 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 speciesTrematomus bernacchii (emerald rockcod)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsIto, N. / Komiyama, N.H. / Fermi, G.
CitationJournal: J.Mol.Biol. / Year: 1995
Title: Structure of deoxyhaemoglobin of the antarctic fish Pagothenia bernacchii with an analysis of the structural basis of the root effect by comparison of the liganded and unliganded haemoglobin structures.
Authors: Ito, N. / Komiyama, N.H. / Fermi, G.
History
DepositionFeb 22, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 17, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Refinement description
Category: pdbx_database_status / software / struct_conn
Item: _pdbx_database_status.process_site / _software.classification / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Refinement description / Category: software / Item: _software.classification
Revision 1.5Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_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

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)66,1398
Polymers63,6734
Non-polymers2,4664
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11810 Å2
ΔGint-103 kcal/mol
Surface area23800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.650, 96.300, 62.650
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.00258, -0.00114, -1), (0.01165, -0.99993, 0.00111), (-0.99993, -0.01165, 0.00259)
Vector: 5.73624, -2.20982, 5.73214)
DetailsTHE COMPLETE TETRAMER (I.E., ASYMMETRIC UNIT) IS GIVEN HERE AND THE TRANSFORMATION PRESENTED ON MTRIX RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR DIMER BC WHEN APPLIED TO DIMER AB.

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Components

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


Mass: 15683.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trematomus bernacchii (emerald rockcod)
References: UniProt: P80043
#2: Protein HEMOGLOBIN (DEOXY) (BETA CHAIN)


Mass: 16153.368 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trematomus bernacchii (emerald rockcod)
References: UniProt: P80044
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.55 %
Crystal
*PLUS
Density % sol: 59 %
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.9 %heamoglobin1drop
210 mMTris-HCl1drop
3100 mM1reservoirKPO4
420 mMIHP1reservoir
56-10 %(w/v)PEG60001reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.2→10 Å / Num. obs: 29393 / % possible obs: 79 % / Observed criterion σ(I): 0
Reflection
*PLUS
Num. measured all: 49914 / Rmerge(I) obs: 0.052
Reflection shell
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 2.3 Å / Rmerge(I) obs: 0.146

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Processing

Software
NameClassification
X-PLORmodel building
PROLSQrefinement
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→10 Å / σ(I): 0
RfactorNum. reflection% reflection
Rfree0.22 --
Rwork0.16 --
obs-29393 79 %
Refinement stepCycle: LAST / Resolution: 2.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4484 0 172 38 4694
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.4872
X-RAY DIFFRACTIONx_mcangle_it2.2833
X-RAY DIFFRACTIONx_scbond_it3.0913
X-RAY DIFFRACTIONx_scangle_it4.994.5

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