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- PDB-1bab: HEMOGLOBIN THIONVILLE: AN ALPHA-CHAIN VARIANT WITH A SUBSTITUTION... -

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Basic information

Entry
Database: PDB / ID: 1bab
TitleHEMOGLOBIN THIONVILLE: AN ALPHA-CHAIN VARIANT WITH A SUBSTITUTION OF A GLUTAMATE FOR VALINE AT NA-1 AND HAVING AN ACETYLATED METHIONINE NH2 TERMINUS
Components
  • HEMOGLOBIN THIONVILLE (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN THIONVILLE (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid 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 / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / 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 / ficolin-1-rich granule lumen / blood microparticle / 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 / 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 beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsKavanaugh, J.S. / Arnone, A.
CitationJournal: J.Biol.Chem. / Year: 1992
Title: Hemoglobin Thionville. An alpha-chain variant with a substitution of a glutamate for valine at NA-1 and having an acetylated methionine NH2 terminus.
Authors: Vasseur, C. / Blouquit, Y. / Kister, J. / Prome, D. / Kavanaugh, J.S. / Rogers, P.H. / Guillemin, C. / Arnone, A. / Galacteros, F. / Poyart, C. / Rosa, J. / Wajcman, H.
History
DepositionMay 6, 1992Processing site: BNL
Revision 1.0Jan 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_planes / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn / struct_ncs_oper / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[1][2] / _atom_sites.fract_transf_matrix[1][3] / _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[2][3] / _atom_sites.fract_transf_matrix[3][1] / _atom_sites.fract_transf_matrix[3][2] / _atom_sites.fract_transf_matrix[3][3] / _atom_sites.fract_transf_vector[1] / _atom_sites.fract_transf_vector[2] / _atom_sites.fract_transf_vector[3] / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.value / _pdbx_validate_planes.rmsd / _pdbx_validate_torsion.phi / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_ncs_oper.matrix[1][1] / _struct_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][2] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _struct_ncs_oper.matrix[3][3] / _struct_ncs_oper.vector[1] / _struct_ncs_oper.vector[2] / _struct_ncs_oper.vector[3] / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Details: Coordinates and associated ncs operations (if present) transformed into standard crystal frame
Provider: repository / Type: Remediation
Revision 2.1Mar 15, 2023Group: Advisory / Category: pdbx_database_remark

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,11410
Polymers62,4564
Non-polymers2,6586
Water4,792266
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12630 Å2
ΔGint-145 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.200, 83.600, 53.800
Angle α, β, γ (deg.)90.00, 99.30, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.949218, 0.312922, -0.029915), (0.313479, 0.931681, -0.184666), (-0.02977, -0.183443, -0.982463)
Vector: 16.90229, 5.07882, 81.81897)
DetailsIN THE ORTHOGONAL COORDINATE SPACE, THE HB TETRAMER HAS BEEN ORIENTED WITH ITS MOLECULAR DYAD ALONG THE Y-AXIS. THUS THE TRANSFORMATION PRESENTED ON *SCALE* RECORDS BELOW IS NOT THE DEFAULT. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR THE A2B2 DIMER WHEN APPLIED TO THE A1B1 DIMER.

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Components

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


Mass: 15337.572 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P69905
#2: Protein HEMOGLOBIN THIONVILLE (DEOXY) (BETA CHAIN)


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / 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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.24 Å3/Da / Density % sol: 45.21 %
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

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.59 Å / Num. obs: 69608 / % possible obs: 93 % / Num. measured all: 754736 / Rmerge(I) obs: 0.054

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.157 / Highest resolution: 1.5 Å
Details: A SECOND CONFORMATION FOR THE AMINO TERMINAL METHIONINE WAS MODELED FOR THE ALPHA 1 SUBUNIT. THIS SECOND CONFORMATION IS REFERRED TO AS "ROT 2" IN THE MANUSCRIPT, WITH THE MAJOR CONFORMATION ...Details: A SECOND CONFORMATION FOR THE AMINO TERMINAL METHIONINE WAS MODELED FOR THE ALPHA 1 SUBUNIT. THIS SECOND CONFORMATION IS REFERRED TO AS "ROT 2" IN THE MANUSCRIPT, WITH THE MAJOR CONFORMATION BEING REFERRED TO AS "ROT 1".
Refinement stepCycle: LAST / Highest resolution: 1.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4410 0 182 266 4858
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0160.01
X-RAY DIFFRACTIONp_angle_d0.0310.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.71.5
X-RAY DIFFRACTIONp_mcangle_it3.82
X-RAY DIFFRACTIONp_scbond_it7.94
X-RAY DIFFRACTIONp_scangle_it11.16
X-RAY DIFFRACTIONp_plane_restr0.0150.01
X-RAY DIFFRACTIONp_chiral_restr0.1620.08
X-RAY DIFFRACTIONp_singtor_nbd0.1650.2
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1340.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.95
X-RAY DIFFRACTIONp_staggered_tor20.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.5 Å / σ(I): 2 / Rfactor obs: 0.157
Solvent computation
*PLUS
Displacement parameters
*PLUS

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