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- PDB-1dxt: HIGH-RESOLUTION X-RAY STUDY OF DEOXY RECOMBINANT HUMAN HEMOGLOBIN... -

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Basic information

Entry
Database: PDB / ID: 1dxt
TitleHIGH-RESOLUTION X-RAY STUDY OF DEOXY RECOMBINANT HUMAN HEMOGLOBINS SYNTHESIZED FROM BETA-GLOBINS HAVING MUTATED AMINO TERMINI
Components
  • HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
  • HEMOGLOBIN (DEOXY) (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 / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / 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 / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / 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: 1.7 Å
AuthorsKavanaugh, J.S. / Arnone, A.
Citation
Journal: Biochemistry / Year: 1992
Title: High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini.
Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A.
#1: Journal: Biochemistry / Year: 1992
Title: Functional Properties of Human Hemoglobins Synthesized from Recombinant Mutant Beta-Globins
Authors: Doyle, M.L. / Lew, G. / Deyoung, A. / Kwiatkowski, L. / Wierzbra, A. / Noble, R.W. / Ackers, G.K.
History
DepositionMay 6, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: 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_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_conn.pdbx_dist_value / _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
Revision 2.2May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)64,8098
Polymers62,3434
Non-polymers2,4664
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11340 Å2
ΔGint-104 kcal/mol
Surface area23460 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. THE A1B1 DIMER CAN BE TRANSFORMED APPROXIMATELY ONTO TO A2B2 DIMER BY THE *MTRIX* RECORDS BELOW.

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Components

#1: Protein HEMOGLOBIN (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) / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein HEMOGLOBIN (DEOXY) (BETA CHAIN)


Mass: 16021.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 227 / 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: 2.25 Å3/Da / Density % sol: 45.3 %
Crystal grow
*PLUS
pH: 7 / Method: microdialysis
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mMammonium phosphate12
2hemoglobin11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.8 Å / Num. obs: 46131 / % possible obs: 90 % / Num. measured all: 148393 / Rmerge(I) obs: 0.034

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.7→6 Å / σ(F): 2 /
RfactorNum. reflection
obs0.16 46508
Refinement stepCycle: LAST / Resolution: 1.7→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4400 0 172 227 4799
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.01
X-RAY DIFFRACTIONp_angle_d0.0290.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0480.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it2.72
X-RAY DIFFRACTIONp_mcangle_it3.73
X-RAY DIFFRACTIONp_scbond_it7.44
X-RAY DIFFRACTIONp_scangle_it10.36
X-RAY DIFFRACTIONp_plane_restr0.0130.01
X-RAY DIFFRACTIONp_chiral_restr0.1640.08
X-RAY DIFFRACTIONp_singtor_nbd0.1670.2
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1580.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.95
X-RAY DIFFRACTIONp_staggered_tor21.115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 1.7 Å / Lowest resolution: 6 Å / Num. reflection obs: 46508 / σ(F): 2 / Rfactor obs: 0.16
Solvent computation
*PLUS
Displacement parameters
*PLUS

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