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- PDB-2hbs: THE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S -

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Basic information

Entry
Database: PDB / ID: 2hbs
TitleTHE HIGH RESOLUTION CRYSTAL STRUCTURE OF DEOXYHEMOGLOBIN S
Components
  • HEMOGLOBIN S (DEOXY), ALPHA CHAIN
  • HEMOGLOBIN S (DEOXY), BETA CHAIN
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN
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 / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / 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 / 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: 2.05 Å
AuthorsHarrington, D.J. / Adachi, K. / Royer Junior, W.E.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The high resolution crystal structure of deoxyhemoglobin S.
Authors: Harrington, D.J. / Adachi, K. / Royer Jr., W.E.
#1: Journal: J.Biol.Chem. / Year: 1985
Title: Refined Crystal Structure of Deoxyhemoglobin S. II. Molecular Interactions in the Crystal
Authors: Padlan, E.A. / Love, W.E.
#2: Journal: J.Biol.Chem. / Year: 1985
Title: Refined Crystal Structure of Deoxyhemoglobin S. I. Restrained Least-Squares Refinement at 3.0-A Resolution
Authors: Padlan, E.A. / Love, W.E.
#3: Journal: Inserm Symp. / Year: 1978
Title: Intermolecular Interactions in Crystals of Human Deoxy Hemoglobin A, C, F and S
Authors: Love, W.E. / Fitzgerald, P.M.D. / Hanson, J.C. / Royer Junior, W.E.
#4: Journal: Proceedings of the Symposium on Molecular and Cellular Aspects of Sickle Cell Disease, Dallas, Texas, December 10, 1975 (in: Dhew Pub (Nih) (Us), No.76-1007)
Year: 1976
Title: Crystal Structure of Sickle-Cell Deoxyhemoglobin
Authors: Wishner, B.C. / Hanson, J.C. / Ringle, W.M. / Love, W.E.
#5: Journal: Proceedings of the First National Symposium on Sickle Cell Disease, Washington, D.C., June 27-29, 1974 (in: Dhew Pub (Nih) (Us), No.75-723)
Year: 1975
Title: Crystals of Deoxy Sickle Cell Hemoglobin
Authors: Wishner, B.C. / Love, W.E.
#6: Journal: J.Mol.Biol. / Year: 1975
Title: Crystal Structure of Sickle-Cell Deoxyhemoglobin at 5 A Resolution
Authors: Wishner, B.C. / Ward, K.B. / Lattman, E.E. / Love, W.E.
History
DepositionMay 6, 1997Processing site: BNL
Revision 1.0Jul 23, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 1, 2017Group: Structure summary
Revision 1.4Feb 14, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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 S (DEOXY), ALPHA CHAIN
B: HEMOGLOBIN S (DEOXY), BETA CHAIN
C: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
D: HEMOGLOBIN S (DEOXY), BETA CHAIN
E: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
F: HEMOGLOBIN S (DEOXY), BETA CHAIN
G: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
H: HEMOGLOBIN S (DEOXY), BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,97416
Polymers124,0428
Non-polymers4,9328
Water10,323573
1
A: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
B: HEMOGLOBIN S (DEOXY), BETA CHAIN
C: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
D: HEMOGLOBIN S (DEOXY), BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4878
Polymers62,0214
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11210 Å2
ΔGint-109 kcal/mol
Surface area23180 Å2
MethodPISA
2
E: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
F: HEMOGLOBIN S (DEOXY), BETA CHAIN
G: HEMOGLOBIN S (DEOXY), ALPHA CHAIN
H: HEMOGLOBIN S (DEOXY), BETA CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4878
Polymers62,0214
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-105 kcal/mol
Surface area23230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.344, 185.681, 52.933
Angle α, β, γ (deg.)90.00, 92.74, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9997, -0.0211, 0.01274), (-0.02101, -0.99975, -0.00726), (0.01289, 0.00699, -0.99989)
Vector: -31.14513, 95.20869, 79.04881)

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Components

#1: Protein
HEMOGLOBIN S (DEOXY), ALPHA CHAIN


Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P69905
#2: Protein
HEMOGLOBIN S (DEOXY), BETA CHAIN


Mass: 15860.216 Da / Num. of mol.: 4 / Mutation: E6V VARIANT / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell: RED BLOOD CELLS / Cellular location: CYTOPLASM / Organ: BLOOD / Tissue: BLOOD / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 573 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

CrystalDensity Matthews: 2.51 Å3/Da / Density % sol: 50.91 %
Description: HIGH RESOLUTION DATA USED TO REFINE 1HBS STRUCTURE
Crystal growpH: 4
Details: HBS WAS SUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 120 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN SOLUTION, 5 ...Details: HBS WAS SUSPENDED IN 30 MM PHOSPHATE BUFFER, PH 7.0, DEOXYGENATED AND CONCENTRATED TO 120 MG/ML. PROTEIN WAS CRYSTALLIZED IN AN ANAEROBIC CHAMBER IN TUBE CONTAINING 10 UL PROTEIN SOLUTION, 5 UL CITRATE BUFFER (PH 4.0), AND 4UL OF 33% PEG 8K, crystallized in anaerobic chamber
Crystal grow
*PLUS
Method: unknown
Details: refer to Wishner, B.C., (1976) Proceedings of the Symposium on Molecular and Cellular Aspects of Sickle Cell Disease, pp. 1-31.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
1120 mg/mlHbS11
230 mMphosphate11

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Mar 9, 1995 / Details: COLLIMATOR
RadiationMonochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→100 Å / Num. obs: 72955 / % possible obs: 95 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 16.1 Å2 / Rsym value: 0.093
Reflection shellResolution: 2.05→2.18 Å / Rsym value: 0.371 / % possible all: 86.1
Reflection
*PLUS
Rmerge(I) obs: 0.093
Reflection shell
*PLUS
% possible obs: 86.1 % / Rmerge(I) obs: 0.371

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementResolution: 2.05→10 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.215 6479 10.1 %RANDOM
Rwork0.165 ---
obs0.165 64050 84.8 %-
Displacement parametersBiso mean: 20.5 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 2.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8760 0 344 573 9677
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d20.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.52
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.941.5
X-RAY DIFFRACTIONx_mcangle_it2.892
X-RAY DIFFRACTIONx_scbond_it3.672
X-RAY DIFFRACTIONx_scangle_it5.392.5
LS refinement shellResolution: 2.05→2.14 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.294 632 10.7 %
Rwork0.247 5270 -
obs--62.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION3PARAM19.SOLTOPH19.SOL
X-RAY DIFFRACTION4PARAM19X.HEMETOPH19X.HEME
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_angle_deg1.49
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg20.3
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.34

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