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- PDB-1sdl: CROSS-LINKED, CARBONMONOXY HEMOGLOBIN A -

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Basic information

Entry
Database: PDB / ID: 1sdl
TitleCROSS-LINKED, CARBONMONOXY HEMOGLOBIN A
Components(HEMOGLOBIN A) x 2
KeywordsOXYGEN TRANSPORT / HEME / RESPIRATORY PROTEIN / ERYTHROCYTE / DISEASE MUTATION / POLYMORPHISM / ACETYLATION
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / 1,3,5-BENZENETRICARBOXYLIC ACID / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 1.8 Å
AuthorsSchumacher, M.A. / Dixon, M.M. / Kluger, R. / Jones, R.T. / Brennan, R.G.
CitationJournal: Nature / Year: 1995
Title: Allosteric transition intermediates modelled by crosslinked haemoglobins.
Authors: Schumacher, M.A. / Dixon, M.M. / Kluger, R. / Jones, R.T. / Brennan, R.G.
History
DepositionFeb 26, 1996Processing site: BNL
Revision 1.0Aug 1, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN A
B: HEMOGLOBIN A
C: HEMOGLOBIN A
D: HEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,86913
Polymers62,0814
Non-polymers2,7889
Water7,188399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12690 Å2
ΔGint-120 kcal/mol
Surface area22950 Å2
MethodPISA
2
A: HEMOGLOBIN A
B: HEMOGLOBIN A
C: HEMOGLOBIN A
D: HEMOGLOBIN A
hetero molecules

A: HEMOGLOBIN A
B: HEMOGLOBIN A
C: HEMOGLOBIN A
D: HEMOGLOBIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,73826
Polymers124,1628
Non-polymers5,57618
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area27090 Å2
ΔGint-255 kcal/mol
Surface area44180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.430, 72.160, 88.030
Angle α, β, γ (deg.)90.00, 108.25, 90.00
Int Tables number5
Space group name H-MC121
DetailsTHERE ARE TWO ALPHA/BETA DIMERS IN THE ASYMMETRIC UNIT.

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein HEMOGLOBIN A


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CROSS-LINKED, CARBONMONOXY / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein HEMOGLOBIN A


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: CROSS-LINKED, CARBONMONOXY / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 408 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-TMM / 1,3,5-BENZENETRICARBOXYLIC ACID


Mass: 210.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 399 / 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: 2.54 Å3/Da / Density % sol: 51.49 %
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
Conc.: 2.35 M / Common name: potassium phosphate

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Data collection

RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionNum. obs: 48608
Reflection
*PLUS
Highest resolution: 1.8 Å / Rmerge(I) obs: 0.063

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Processing

SoftwareName: TNT / Classification: refinement
RefinementHighest resolution: 1.8 Å / σ(F): 1 /
RfactorNum. reflection
Rwork0.15 -
obs-48608
Refinement stepCycle: LAST / Highest resolution: 1.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 193 399 4976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.1
X-RAY DIFFRACTIONt_angle_deg2.34
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Rfactor obs: 0.15
Solvent computation
*PLUS
Displacement parameters
*PLUS

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