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- PDB-1a3o: ARTIFICIAL MUTANT (ALPHA Y42H) OF DEOXY HEMOGLOBIN -

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Basic information

Entry
Database: PDB / ID: 1a3o
TitleARTIFICIAL MUTANT (ALPHA Y42H) OF DEOXY HEMOGLOBIN
Components
  • HEMOGLOBIN (ALPHA CHAIN)
  • HEMOGLOBIN (BETA CHAIN)
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / 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 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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsTame, J. / Vallone, B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2000
Title: The structures of deoxy human haemoglobin and the mutant Hb Tyralpha42His at 120 K.
Authors: Tame, J.R. / Vallone, B.
History
DepositionJan 22, 1998Processing site: BNL
Revision 1.0Apr 29, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 3, 2021Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / 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 / _pdbx_database_status.process_site / _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
Revision 1.4Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,4978
Polymers62,0314
Non-polymers2,4664
Water7,422412
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-109 kcal/mol
Surface area23200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.440, 81.160, 53.320
Angle α, β, γ (deg.)90.00, 99.65, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein HEMOGLOBIN (ALPHA CHAIN)


Mass: 15125.327 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, Y42H / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED CELL / Tissue: BLOOD / References: UniProt: P69905
#2: Protein HEMOGLOBIN (BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 2 / Mutation: CHAIN A, C, Y42H / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED CELL / Tissue: BLOOD / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal grow
*PLUS
pH: 6.5 / Method: unknown / Details: Perutz, M.F., (1968) J. Cryst. Growth, 2, 54.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14 Mammonium sulfate11
22 M11(NH4)H2PO4
32 M11(NH4)2HPO4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: May 1, 1997 / Details: MIRROR
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→15 Å / Num. obs: 49373 / % possible obs: 96.02 % / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18
Reflection shellResolution: 1.8→1.87 Å / Redundancy: 1.36 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 2.9 / % possible all: 74.2
Reflection shell
*PLUS
% possible obs: 76.4 %

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.8→15 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.22653 2378 5 %
Rwork0.17994 --
obs-45030 96.02 %
Displacement parametersBiso mean: 21.1 Å2
Refinement stepCycle: LAST / Resolution: 1.8→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4372 0 172 412 4956
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0310.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0360.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.1632
X-RAY DIFFRACTIONp_mcangle_it2.6873
X-RAY DIFFRACTIONp_scbond_it2.8662
X-RAY DIFFRACTIONp_scangle_it4.0463
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.0970.15
X-RAY DIFFRACTIONp_singtor_nbd0.1680.3
X-RAY DIFFRACTIONp_multtor_nbd0.2750.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1060.3
X-RAY DIFFRACTIONp_planar_tor37
X-RAY DIFFRACTIONp_staggered_tor15.915
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.920
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 45030 / Rfactor obs: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS

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