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- PDB-2hbd: HIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKY... -

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Basic information

Entry
Database: PDB / ID: 2hbd
TitleHIGH RESOLUTION X-RAY STRUCTURES OF MYOGLOBIN-AND HEMOGLOBIN-ALKYL ISOCYANIDE COMPLEXES
Components
  • HEMOGLOBIN A (METHYL ISOCYANIDE) (ALPHA CHAIN)
  • HEMOGLOBIN A (METHYL ISOCYANIDE) (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 / 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 / METHYL ISOCYANIDE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsJohnson, K.A. / Olson, J.S. / Phillips Jr., G.N.
Citation
Journal: Thesis / Year: 1993
Title: High Resolution X-Ray Structures of Myoglobin-and Hemoglobin-Alkyl Isocyanide Complexes
Authors: Johnson, K.A.
#1: Journal: J.Mol.Biol. / Year: 1989
Title: Structure of Myoglobin-Ethyl Isocyanide: Histidine as a Swinging Door for Ligand Entry
Authors: Johnson, K.A. / Olson, J.S. / Phillips Jr., G.N.
History
DepositionAug 31, 1994Processing site: BNL
Revision 1.0Feb 7, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 27, 2019Group: Advisory / Derived calculations / Other
Category: pdbx_database_status / pdbx_distant_solvent_atoms ...pdbx_database_status / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 A (METHYL ISOCYANIDE) (ALPHA CHAIN)
B: HEMOGLOBIN A (METHYL ISOCYANIDE) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3566
Polymers31,0412
Non-polymers1,3154
Water1,18966
1
A: HEMOGLOBIN A (METHYL ISOCYANIDE) (ALPHA CHAIN)
B: HEMOGLOBIN A (METHYL ISOCYANIDE) (BETA CHAIN)
hetero molecules

A: HEMOGLOBIN A (METHYL ISOCYANIDE) (ALPHA CHAIN)
B: HEMOGLOBIN A (METHYL ISOCYANIDE) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,71112
Polymers62,0814
Non-polymers2,6308
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11860 Å2
ΔGint-103 kcal/mol
Surface area23830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.050, 54.050, 193.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein HEMOGLOBIN A (METHYL ISOCYANIDE) (ALPHA CHAIN)


Mass: 15150.353 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: SEED / References: UniProt: P69905
#2: Protein HEMOGLOBIN A (METHYL ISOCYANIDE) (BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Organ: SEED / References: UniProt: P68871
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-MNC / METHYL ISOCYANIDE


Mass: 41.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3N
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.03 %

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.2→5 Å / Rfactor Rwork: 0.176 / Rfactor obs: 0.176 / σ(F): 0
Details: REFINEMENT. THE STARTING MODEL WAS THE ETHYL ISOCYANIDE - HEMOGLOBIN (1HBC) COMPLEX WITH THE LIGAND REMOVED AND THE METHYL ISOCYANIDE LIGAND MODELED INTO INITIAL DIFFERENCE MAP (FO-FC) ...Details: REFINEMENT. THE STARTING MODEL WAS THE ETHYL ISOCYANIDE - HEMOGLOBIN (1HBC) COMPLEX WITH THE LIGAND REMOVED AND THE METHYL ISOCYANIDE LIGAND MODELED INTO INITIAL DIFFERENCE MAP (FO-FC) ELECTRON DENSITY. THE PROGRAM X-PLOR WAS USED TO ACHIEVE A FINAL CONVENTIONAL R- FACTOR OF 17.6%. THE REFINEMENT PROCESS INCLUDED SIMULATED ANNEALING FOLLOWED BY POSITION AND TEMPERATURE FACTOR REFINEMENT. AN ITERATIVE PROCESS OF MANUAL REFITTING OF SIDE CHAINS AND PLACEMENT OF WATERS WAS PERFORMED UNTIL THE R-FACTOR CONVERGED. THE WEIGHTING OF PSEUDO-ENERGY X-RAY TERM WAS ADJUSTED TO GIVE A BOND RMS OF 0.020 ANGSTROMS IN THE LAST FEW STEPS OF POSITIONAL REFINEMENT. WATERS (N=109) WERE RETAINED FROM THE STARTING STRUCTURE OF OXYHEMOGLOBIN (1HHO). ADDITIONAL WATERS WERE ADDED IF THEY LAY IN 3.5 - 4.O SIGMA PEAKS IN FO-FC ELECTRON DENSITY MAPS AND 1 SIGMA PEAKS IN 2FO-FC MAPS. CONCURRENTLY, A WATER WOULD BE DELETED IF ITS OCCUPANCY (Q) AND TEMPERATURE FACTOR (B) COMBINED TO MAKE THE VALUE (Q*EXP(- B/36)*100%) FALL BELOW 10%. A PEAK NUMBER OF 104 WATERS WAS REACHED. THIS WAS REDUCED TO 66 WATERS OVER THE LAST FEW REFINEMENT CYCLES BY DELETING WATERS WHICH FELL BELOW A 20% THRESHOLD.
Refinement stepCycle: LAST / Resolution: 2.2→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 92 66 2350
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.02
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_deg2.193
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_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it22
X-RAY DIFFRACTIONx_scbond_it22
X-RAY DIFFRACTIONx_scangle_it2.52.5

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