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- PDB-1g0b: CARBONMONOXY LIGANDED EQUINE HEMOGLOBIN PH 8.5 -

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Basic information

Entry
Database: PDB / ID: 1g0b
TitleCARBONMONOXY LIGANDED EQUINE HEMOGLOBIN PH 8.5
Components
  • HEMOGLOBIN ALPHA CHAIN
  • HEMOGLOBIN BETA CHAIN
KeywordsOXYGEN STORAGE/TRANSPORT / equine / hemoglobin / liganded / carbonmonoxy / protoporphyrin IX / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsMueser, T.C. / Rogers, P.H. / Arnone, A.
Citation
Journal: Biochemistry / Year: 2000
Title: Interface sliding as illustrated by the multiple quaternary structures of liganded hemoglobin.
Authors: Mueser, T.C. / Rogers, P.H. / Arnone, A.
#1: Journal: J.Mol.Biol. / Year: 1977
Title: The structure of horse methaemoglobin at 2-0 A resolution.
Authors: Ladner, R.C. / Heidner, E.J. / Perutz, M.F.
History
DepositionOct 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 10, 2011Group: Other
Revision 1.4Feb 7, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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
Remark 999SEQUENCE The sequence is the same as in pdb entry 2MHB. This 1g0b structure is a re-refined ...SEQUENCE The sequence is the same as in pdb entry 2MHB. This 1g0b structure is a re-refined structure of R.C.LADNER,E.G.HEIDNER,M.F.PERUTZ from 1977.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4606
Polymers31,1712
Non-polymers1,2894
Water1,29772
1
A: HEMOGLOBIN ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
hetero molecules

A: HEMOGLOBIN ALPHA CHAIN
B: HEMOGLOBIN BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,91912
Polymers62,3414
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Unit cell
Length a, b, c (Å)108.800, 63.200, 54.600
Angle α, β, γ (deg.)90.00, 110.70, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer constructed from the heterodimer of chain A (alpha) and chain B (beta) and a symmetry related heterodimer of chain A (alpha) and chain B (beta)

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Components

#1: Protein HEMOGLOBIN ALPHA CHAIN


Mass: 15138.280 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: BLOOD / References: UniProt: P01958
#2: Protein HEMOGLOBIN BETA CHAIN


Mass: 16032.274 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue: BLOOD / References: UniProt: P02062
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.33 % / Description: AUTHOR USED THE SF DATA FROM ENTRY 2MHB.
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12.0 Mammonium sulfate1reservoir
2100 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Num. measured all: 316145
Reflection shell
*PLUS
% possible obs: 87.8 %

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Processing

Software
NameClassification
MERLOTphasing
PROLSQrefinement
RefinementResolution: 1.9→8 Å / σ(F): 2 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.178 --
all0.178 25687 -
obs0.178 25529 99.38 %
Refinement stepCycle: LAST / Resolution: 1.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2203 0 90 72 2365
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.1
X-RAY DIFFRACTIONp_angle_d0.024
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.8 Å2

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