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- PDB-1thb: REFINEMENT OF A PARTIALLY OXYGENATED T STATE HAEMOGLOBIN AT 1.5 A... -

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Basic information

Entry
Database: PDB / ID: 1thb
TitleREFINEMENT OF A PARTIALLY OXYGENATED T STATE HAEMOGLOBIN AT 1.5 ANGSTROMS RESOLUTION
Components(HEMOGLOBIN A ...) x 2
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 / INOSITOL HEXAKISPHOSPHATE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.5 Å
AuthorsWaller, D.A. / Liddington, R.C.
CitationJournal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Refinement of a partially oxygenated T state human haemoglobin at 1.5 A resolution.
Authors: Waller, D.A. / Liddington, R.C.
History
DepositionJan 23, 1990Processing site: BNL
Revision 1.0Jan 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 17, 2012Group: Advisory
Revision 2.0Feb 8, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / chem_comp / database_2 / database_PDB_matrix / pdbx_database_status / pdbx_struct_conn_angle / pdbx_validate_planes / pdbx_validate_rmsd_angle / 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_vector[1] / _atom_sites.fract_transf_vector[2] / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _pdbx_database_status.process_site / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_validate_planes.rmsd / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_oper.matrix[1][2] / _struct_ncs_oper.matrix[1][3] / _struct_ncs_oper.matrix[2][1] / _struct_ncs_oper.matrix[2][3] / _struct_ncs_oper.matrix[3][1] / _struct_ncs_oper.matrix[3][2] / _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 A (OXY) (ALPHA CHAIN)
B: HEMOGLOBIN A (DEOXY) (BETA CHAIN)
C: HEMOGLOBIN A (OXY) (ALPHA CHAIN)
D: HEMOGLOBIN A (DEOXY) (BETA CHAIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,27111
Polymers62,0814
Non-polymers3,1907
Water5,657314
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.800, 97.800, 65.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Atom site foot note1: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY ...1: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY AFTER REPEATED EXAMINATION INCLUDING THE USE OF OMIT MAPS.
2: IHP HAS NOT BEEN REFINED OR INCLUDED IN ANY MAP CALCULATION. IHP IS INCLUDED ONLY TO AID IN VISUALIZATION OF WEAK ELECTRON DENSITY AND FOR ILLUSTRATION OF THE BINDING SITE.
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.774, -0.464979, -0.428988), (-0.465021, -0.878, 0.113002), (-0.430012, 0.111998, -0.896)
Vector: 24.97112, 59.69436, 38.12008)

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Components

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HEMOGLOBIN A ... , 2 types, 4 molecules ACBD

#1: Protein HEMOGLOBIN A (OXY) (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 A (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

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Non-polymers , 4 types, 321 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#5: Chemical ChemComp-IHP / INOSITOL HEXAKISPHOSPHATE / MYO-INOSITOL HEXAKISPHOSPHATE / INOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE


Mass: 660.035 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H18O24P6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 314 / 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: 2.47 Å3/Da / Density % sol: 50.21 %
Crystal grow
*PLUS
Method: batch method / PH range low: 7.4 / PH range high: 7.2
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118-25 %(v/v)PEG100011
2inoaitol hexaphosphate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.5 Å / Num. obs: 73013 / Observed criterion σ(I): 3 / Rmerge(I) obs: 0.14 / Biso Wilson estimate: 32.3 Å2

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 1.5→10 Å / Rfactor obs: 0.196
Details: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE ...Details: HIS D 2 AND ITS NEIGHBORS ARE VERY POORLY ORDERED IN DENSITY MAPS AND THIS IS REFLECTED IN THE TEMPERATURE FACTORS. HOWEVER, THE CONFORMATION DEPICTED IS THAT WHICH BEST FITS THE AVAILABLE DENSITY AFTER REPEATED EXAMINATION INCLUDING THE USE OF OMIT MAPS. IHP HAS NOT BEEN REFINED OR INCLUDED IN ANY MAP CALCULATION. IHP IS INCLUDED ONLY TO AID IN VISUALIZATION OF WEAK ELECTRON DENSITY AND FOR ILLUSTRATION OF THE BINDING SITE.
Refinement stepCycle: LAST / Resolution: 1.5→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 212 314 4910
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0250.02
X-RAY DIFFRACTIONp_angle_d0.0640.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0750.06
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr0.0190.02
X-RAY DIFFRACTIONp_chiral_restr0.1730.12
X-RAY DIFFRACTIONp_singtor_nbd0.210.5
X-RAY DIFFRACTIONp_multtor_nbd0.2220.5
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1890.5
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor4.720
X-RAY DIFFRACTIONp_staggered_tor20.120
X-RAY DIFFRACTIONp_orthonormal_tor34.920
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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