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- PDB-7dy4: High resolution crystal structure of hemoglobin M Boston. -

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Basic information

Entry
Database: PDB / ID: 7dy4
TitleHigh resolution crystal structure of hemoglobin M Boston.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Hemoglobin / Abnormal Hemoglobin / Allosteric proteins / Oxygen binding
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
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: 1.3 Å
AuthorsOhki, M. / Park, S.-Y.
CitationJournal: To Be Published
Title: High resolution crystal structure of hemoglobin M Boston.
Authors: Nagatomo, S. / Naoya, S. / Ohki, M. / Park, S.Y.
History
DepositionJan 20, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 26, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,19416
Polymers124,2628
Non-polymers4,9328
Water37,0032054
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5978
Polymers62,1314
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11120 Å2
ΔGint-108 kcal/mol
Surface area23730 Å2
MethodPISA
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5978
Polymers62,1314
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11190 Å2
ΔGint-106 kcal/mol
Surface area23610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.115, 86.583, 121.388
Angle α, β, γ (deg.)90.000, 99.306, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein
Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15175.380 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 4 / 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.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2054 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.43 Å3/Da / Density % sol: 49.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20% w/v PEG 3350, 0.1M Bistris-HCl buffer, 0.2M magnesium chloride, pH 6.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: DECTRIS PILATUS3 X 200K-A / Detector: PIXEL / Date: Jun 10, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.3→13.16 Å / Num. obs: 277356 / % possible obs: 95.5 % / Redundancy: 3.1 % / Biso Wilson estimate: 9.03 Å2 / CC1/2: 0.998 / Net I/σ(I): 17
Reflection shellResolution: 1.3→1.35 Å / Num. unique obs: 854995 / CC1/2: 0.949

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
CrysalisProdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2dn2

2dn2


Resolution: 1.3→13.16 Å / SU ML: 0.1038 / Cross valid method: FREE R-VALUE / σ(F): 1.89 / Phase error: 18.1241
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1863 13918 5.05 %
Rwork0.1657 261623 -
obs0.1667 275541 94.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 14.36 Å2
Refinement stepCycle: LAST / Resolution: 1.3→13.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8776 0 344 2054 11174
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00629408
X-RAY DIFFRACTIONf_angle_d1.159412912
X-RAY DIFFRACTIONf_chiral_restr0.12441400
X-RAY DIFFRACTIONf_plane_restr0.00711612
X-RAY DIFFRACTIONf_dihedral_angle_d12.85241264
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.310.24013890.20267815X-RAY DIFFRACTION84.71
1.31-1.330.22184340.20127830X-RAY DIFFRACTION85.23
1.33-1.350.21234200.19597859X-RAY DIFFRACTION86.24
1.35-1.360.20054490.1917905X-RAY DIFFRACTION86.79
1.36-1.380.19844330.18978059X-RAY DIFFRACTION87.71
1.38-1.40.19154460.18788079X-RAY DIFFRACTION88.78
1.4-1.420.21074360.18828255X-RAY DIFFRACTION89.59
1.42-1.440.20944240.18528229X-RAY DIFFRACTION90.41
1.44-1.460.20214550.18068434X-RAY DIFFRACTION91.45
1.46-1.490.20334470.17788449X-RAY DIFFRACTION92.4
1.49-1.510.20824610.17388491X-RAY DIFFRACTION93.17
1.51-1.540.18544480.17138667X-RAY DIFFRACTION94.13
1.54-1.570.19194520.16688694X-RAY DIFFRACTION94.51
1.57-1.60.18814670.16778787X-RAY DIFFRACTION95.89
1.6-1.640.1944560.16938859X-RAY DIFFRACTION96.64
1.64-1.680.19574890.17298927X-RAY DIFFRACTION97.55
1.68-1.720.19424650.16889030X-RAY DIFFRACTION98.27
1.72-1.760.19614740.17159118X-RAY DIFFRACTION98.81
1.76-1.820.18874820.17359101X-RAY DIFFRACTION99.22
1.82-1.870.20514740.17089088X-RAY DIFFRACTION99.16
1.87-1.940.18525080.16789103X-RAY DIFFRACTION99.34
1.94-2.020.19534880.1669155X-RAY DIFFRACTION99.55
2.02-2.110.16964810.15369140X-RAY DIFFRACTION99.87
2.11-2.220.18235080.15599198X-RAY DIFFRACTION99.73
2.22-2.360.17555020.15939114X-RAY DIFFRACTION99.66
2.36-2.540.20184570.16939269X-RAY DIFFRACTION99.78
2.54-2.790.19264860.16939194X-RAY DIFFRACTION99.77
2.79-3.190.17644810.16449218X-RAY DIFFRACTION99.76
3.19-40.15944860.14589269X-RAY DIFFRACTION99.9
4-13.160.17445200.15329287X-RAY DIFFRACTION99.24

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