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- PDB-1y0d: T-to-THigh Quaternary Transitions in Human Hemoglobin: desArg141a... -

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Basic information

Entry
Database: PDB / ID: 1y0d
TitleT-to-THigh Quaternary Transitions in Human Hemoglobin: desArg141alpha deoxy low-salt
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsTRANSPORT PROTEIN / hemoglobin mutant / globin
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / 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 / 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 ...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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKavanaugh, J.S. / Rogers, P.H. / Arnone, A.
Citation
Journal: Biochemistry / Year: 2005
Title: Crystallographic evidence for a new ensemble of ligand-induced allosteric transitions in hemoglobin: the T-to-T(high) quaternary transitions.
Authors: Kavanaugh, J.S. / Rogers, P.H. / Arnone, A.
#1: Journal: J.Mol.Biol. / Year: 1995
Title: Structure and Oxygen Affinity of Crystalline DesArg141alpha Human Hemoglobin A in the T State
Authors: Kavanaugh, J.S. / Chafin, D.R. / Arnone, A. / Mozzarelli, A. / Rivetti, C. / Luigi Rossi, G. / Kwiatkowski, L.D. / Noble, R.W.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: RCSB
SupersessionNov 30, 2004ID: 1DSH
Revision 1.0Nov 30, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2338
Polymers61,7674
Non-polymers2,4664
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10580 Å2
ΔGint-107 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.900, 99.000, 65.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Detailsthe crystallogrphic asymmetric unit in this entry is an alpha2beta2 tetramer. the biological unit is an alpha2beta2 tetramer. the crystallographic asymmetric unit and the biological unit are equivalent

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Components

#1: Protein Hemoglobin alpha chain


Mass: 14993.159 Da / Num. of mol.: 2 / Fragment: Residues 1-140 / Source method: isolated from a natural source
Details: Arg141 is removed by enzymatic digestion with carboxypeptidase B
Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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.: 194 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growTemperature: 298 K / pH: 7
Details: 10% PEG 6000, 10 mM potassium phosphate, 100 mM potassium chloride, 3 mM sodium dithionite, 10 mg/ml Hb, pH 7.0, batch, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Oct 10, 1992 / Details: GRAPHITE
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 36277 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 7 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 12.2
Reflection shellResolution: 2.1→2.27 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.189 / Mean I/σ(I) obs: 2.2 / % possible all: 86.5

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Processing

Software
NameClassification
SDMSdata collection
SDMSdata reduction
X-PLORmodel building
PROLSQrefinement
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XXT

1xxt


Resolution: 2.1→10 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.242 3132 10 %MATCHED TO PDB ENTRY 1XXT
Rwork0.175 ---
all-35713 --
obs-34434 97.2 %-
Displacement parametersBiso mean: 25.05 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 172 194 4724
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0110.01
X-RAY DIFFRACTIONp_angle_d0.0270.015
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0430.03
X-RAY DIFFRACTIONp_hb_or_metal_coord0.130.1
X-RAY DIFFRACTIONp_mcbond_it2.3592
X-RAY DIFFRACTIONp_mcangle_it3.0273
X-RAY DIFFRACTIONp_scbond_it5.3874
X-RAY DIFFRACTIONp_scangle_it7.0756
X-RAY DIFFRACTIONp_plane_restr0.0110.01
X-RAY DIFFRACTIONp_chiral_restr0.1350.1
X-RAY DIFFRACTIONp_singtor_nbd0.1610.2
X-RAY DIFFRACTIONp_multtor_nbd0.1670.2
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1870.2
X-RAY DIFFRACTIONp_planar_tor2.45
X-RAY DIFFRACTIONp_staggered_tor2115
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor32.325
X-RAY DIFFRACTIONp_special_tor
LS refinement shellResolution: 2.1→2.27 Å
RfactorNum. reflection% reflection
Rfree0.283 592 -
Rwork0.238 --
obs--86.5 %

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