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- PDB-1cbl: THE 1.9 ANGSTROM STRUCTURE OF DEOXY-BETA4 HEMOGLOBIN: ANALYSIS OF... -

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Basic information

Entry
Database: PDB / ID: 1cbl
TitleTHE 1.9 ANGSTROM STRUCTURE OF DEOXY-BETA4 HEMOGLOBIN: ANALYSIS OF THE PARTITIONING OF QUATERNARY-ASSOCIATED AND LIGAND-INDUCED CHANGES IN TERTIARY STRUCTURE
ComponentsHEMOGLOBIN BETA 4 (DEOXY)
KeywordsOXYGEN TRANSPORT
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / cytosol
Similarity search - Function
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
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsBorgstahl, G.E.O. / Arnone, A.
CitationJournal: J.Mol.Biol. / Year: 1994
Title: The 1.9 A structure of deoxy beta 4 hemoglobin. Analysis of the partitioning of quaternary-associated and ligand-induced changes in tertiary structure.
Authors: Borgstahl, G.E. / Rogers, P.H. / Arnone, A.
History
DepositionFeb 18, 1993Processing site: BNL
Revision 1.0Jul 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
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_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 / _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_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

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Assembly

Deposited unit
A: HEMOGLOBIN BETA 4 (DEOXY)
B: HEMOGLOBIN BETA 4 (DEOXY)
C: HEMOGLOBIN BETA 4 (DEOXY)
D: HEMOGLOBIN BETA 4 (DEOXY)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,41112
Polymers63,5614
Non-polymers2,8508
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12560 Å2
ΔGint-188 kcal/mol
Surface area22290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.000, 81.800, 54.400
Angle α, β, γ (deg.)90.00, 89.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
HEMOGLOBIN BETA 4 (DEOXY)


Mass: 15890.198 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: P68871
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#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.: 71 / 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: 2.2 Å3/Da / Density % sol: 44.2 %
Crystal grow
*PLUS
Method: batch method
Details: batch crystallization solution were prepared in a nitrogen-filled globe box
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
11 %Hb11
22.04 Msulfate11
30.26 Mphosphate11
49 mMferrous citrate11

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.83 Å / Num. obs: 46515 / % possible obs: 95.2 % / Num. measured all: 352416 / Rmerge(I) obs: 0.0521

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Processing

Software
NameClassification
PROLSQrefinement
TNTrefinement
RefinementResolution: 1.8→10 Å / σ(F): 2
Details: THE ORTHOGONAL COORDINATE FRAME USED IN THIS ENTRY IS NOT THE DEFAULT ORTHOGONAL COORDINATE FRAME FOR SPACE GROUP P 21.
RfactorNum. reflection
obs0.19 46515
Refinement stepCycle: LAST / Resolution: 1.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4492 0 192 71 4755
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.01
X-RAY DIFFRACTIONp_angle_d0.0330.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0540.03
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it3.52
X-RAY DIFFRACTIONp_mcangle_it5.13
X-RAY DIFFRACTIONp_scbond_it9.24
X-RAY DIFFRACTIONp_scangle_it13.46
X-RAY DIFFRACTIONp_plane_restr0.0130.01
X-RAY DIFFRACTIONp_chiral_restr0.1640.08
X-RAY DIFFRACTIONp_singtor_nbd0.1830.2
X-RAY DIFFRACTIONp_multtor_nbd0.1910.2
X-RAY DIFFRACTIONp_xhyhbond_nbd0.1730.2
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor3.75
X-RAY DIFFRACTIONp_staggered_tor22.215
X-RAY DIFFRACTIONp_orthonormal_tor31.125
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Rfactor obs: 0.19 / Highest resolution: 1.9 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 32.8 Å2

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