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- PDB-1hba: HIGH-RESOLUTION X-RAY STUDY OF DEOXYHEMOGLOBIN ROTHSCHILD 37BETA ... -

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Basic information

Entry
Database: PDB / ID: 1hba
TitleHIGH-RESOLUTION X-RAY STUDY OF DEOXYHEMOGLOBIN ROTHSCHILD 37BETA TRP-> ARG: A MUTATION THAT CREATES AN INTERSUBUNIT CHLORIDE-BINDING SITE
Components
  • HEMOGLOBIN ROTHSCHILD (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN ROTHSCHILD (DEOXY) (BETA CHAIN)
KeywordsOXYGEN TRANSPORT
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: 2.1 Å
AuthorsKavanaugh, J.S. / Arnone, A.
Citation
Journal: Biochemistry / Year: 1992
Title: High-resolution X-ray study of deoxyhemoglobin Rothschild 37 beta Trp----Arg: a mutation that creates an intersubunit chloride-binding site.
Authors: Kavanaugh, J.S. / Rogers, P.H. / Case, D.A. / Arnone, A.
#1: Journal: J.Mol.Biol. / Year: 1984
Title: The Crystal Structure of Human Deoxyheamoglobin at 1.74 Angstroms Resolution
Authors: Fermi, G. / Perutz, M.F. / Shaanan, B.
#2: Journal: J.Biol.Chem. / Year: 1987
Title: Specifically Carboxymethylated Hemoglobin as an Analogue of Carbamino Hemoglobin: Solution and X-Ray Studies of Carboxymethylated Hemoglobin and X-Ray Studies of Carbamino Hemoglobin
Authors: Fantl, W.J. / Didonato, A. / Manning, J.M. / Rogers, P.H. / Arnone, A.
History
DepositionJan 7, 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_ref_seq_dif / 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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _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 ROTHSCHILD (DEOXY) (ALPHA CHAIN)
B: HEMOGLOBIN ROTHSCHILD (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN ROTHSCHILD (DEOXY) (ALPHA CHAIN)
D: HEMOGLOBIN ROTHSCHILD (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,56010
Polymers62,0234
Non-polymers2,5376
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11650 Å2
ΔGint-127 kcal/mol
Surface area23000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.000, 99.300, 66.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.775363, 0.457539, -0.4323), (0.461844, -0.880976, -0.112459), (-0.433729, -0.111779, -0.894387)
Vector: -14.1136, 38.24767, -17.4808)

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Components

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


Mass: 15150.353 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 ROTHSCHILD (DEOXY) (BETA CHAIN)


Mass: 15861.183 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-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O
Compound detailsHEMOGLOBIN ROTHSCHILD IS A NATURAL MUTANT IN WHICH TRP 37 OF EACH BETA CHAIN IS REPLACED BY AN ARG. ...HEMOGLOBIN ROTHSCHILD IS A NATURAL MUTANT IN WHICH TRP 37 OF EACH BETA CHAIN IS REPLACED BY AN ARG. THE MUTATION CREATES AN INTERSUBUNIT CHLORIDE BINDING SITE (CHLORIDES 200 AND 201).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.98 %
Crystal grow
*PLUS
Method: batch method / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlhemoglobin11
210 mMpotassium phosphate11
3100 mMpotassium chloride11
44 mMsodium dithionite11
510-10.5 %PEG600011

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 33303 / % possible obs: 77 % / Num. measured all: 101776 / Rmerge(I) obs: 0.043

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.176 / Highest resolution: 2.1 Å
Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM THAT IS STANDARD FOR TETRAMERIC HEMOGLOBINS. THE Y AXIS IS A NONCRYSTALLOGRAPHIC MOLECULAR DIAD, AND THE X AXIS IS A PSEUDO ...Details: THE COORDINATES GIVEN HERE ARE IN THE ORTHOGONAL ANGSTROM SYSTEM THAT IS STANDARD FOR TETRAMERIC HEMOGLOBINS. THE Y AXIS IS A NONCRYSTALLOGRAPHIC MOLECULAR DIAD, AND THE X AXIS IS A PSEUDO DIAD THAT RELATES THE ALPHA-1 SUBUNIT TO THE BETA-1 SUBUNIT (AND ALPHA-2 TO BETA-2). COORDINATES ARE GIVEN FOR THE FULL TETRAMER. SUBUNIT LABELS A, B, C, AND D REFER TO SUBUNITS A1, B1, A2, AND B2, RESPECTIVELY. THE TRANSFORMATION PRESENTED ON *MTRIX* RECORDS BELOW WILL GENERATE APPROXIMATE COORDINATES FOR THE ALPHA2-BETA2 DIMER WHEN APPLIED TO THE ALPHA1-BETA1 DIMER. THE CELL DIMENSIONS PRESENTED ON THE CRYST1 RECORD BELOW ARE THOSE THAT WERE USED IN THE REFINEMENT. PLEASE NOTE THAT SOME DIFFERENCES EXIST IN THE FIRST DECIMAL PLACE BETWEEN THESE VALUES AND THE CELL DIMENSIONS PUBLISHED IN THE 1992 BIOCHEMISTRY PAPER.
Refinement stepCycle: LAST / Highest resolution: 2.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4378 0 174 201 4753
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.01
X-RAY DIFFRACTIONp_angle_d0.0250.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0420.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.91.5
X-RAY DIFFRACTIONp_mcangle_it2.82
X-RAY DIFFRACTIONp_scbond_it6.94
X-RAY DIFFRACTIONp_scangle_it9.76
X-RAY DIFFRACTIONp_plane_restr0.010.01
X-RAY DIFFRACTIONp_chiral_restr0.1310.08
X-RAY DIFFRACTIONp_singtor_nbd0.1650.2
X-RAY DIFFRACTIONp_multtor_nbd0.1820.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1740.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor2.55
X-RAY DIFFRACTIONp_staggered_tor20.215
X-RAY DIFFRACTIONp_orthonormal_tor2925
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 8 Å / Num. reflection obs: 30741 / σ(F): 2 / Rfactor obs: 0.176
Solvent computation
*PLUS
Displacement parameters
*PLUS

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