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- PDB-7qu4: Recombinant Human Fetal Hemoglobin mutant - alpha subunit mutatio... -

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Basic information

Entry
Database: PDB / ID: 7qu4
TitleRecombinant Human Fetal Hemoglobin mutant - alpha subunit mutations K11E,K56E,N78D,K90E
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit gamma-2
KeywordsOXYGEN TRANSPORT / Globin / Hemoglobin
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / 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 / Cytoprotection by HMOX1 / oxygen binding / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / inflammatory response / heme binding / 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 gamma-2 / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å
AuthorsKettisen, K. / Nyblom, M. / Bulow, L.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research CouncilVR 5607-2014,VR 2019-03996 Sweden
The Swedish Foundation for Strategic ResearchRBP14-0055 Sweden
CitationJournal: Front Mol Biosci / Year: 2023
Title: Structural and oxidative investigation of a recombinant high-yielding fetal hemoglobin mutant.
Authors: Kettisen, K. / Nyblom, M. / Smeds, E. / Fago, A. / Bulow, L.
History
DepositionJan 17, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2023Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 7, 2024Group: 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
G: Hemoglobin subunit gamma-2
H: Hemoglobin subunit gamma-2
A: Hemoglobin subunit alpha
B: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3278
Polymers62,8624
Non-polymers2,4664
Water10,178565
1
G: Hemoglobin subunit gamma-2
B: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6644
Polymers31,4312
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-50 kcal/mol
Surface area13150 Å2
MethodPISA
2
H: Hemoglobin subunit gamma-2
A: Hemoglobin subunit alpha
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6644
Polymers31,4312
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-49 kcal/mol
Surface area13230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.450, 189.200, 66.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain 'A' and (resid 1 through 141 or resid 143))A1 - 140
121(chain 'A' and (resid 1 through 141 or resid 143))A143
231chain 'B'B1 - 140
241chain 'B'B143
152chain 'G'G3 - 144
162chain 'G'G147
272(chain 'H' and resid 3 through 147)H3 - 144
282(chain 'H' and resid 3 through 147)H147

NCS ensembles :
ID
1
2

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Components

#1: Protein Hemoglobin subunit gamma-2 / Gamma-2-globin / Hb F Ggamma / Hemoglobin gamma-2 chain / Hemoglobin gamma-G chain


Mass: 16148.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69892
#2: Protein Hemoglobin subunit alpha / Alpha-globin / Hemoglobin alpha chain


Mass: 15282.337 Da / Num. of mol.: 2 / Mutation: K11E,K56E,N78D,K90E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.2 M Sodium fluoride, 0.1 M Bis-Tris propane pH 6.5, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.97625 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.657→54.463 Å / Num. obs: 72637 / % possible obs: 98.9 % / Redundancy: 13.6 % / Biso Wilson estimate: 25.68 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.067 / Net I/σ(I): 21.2
Reflection shellResolution: 1.657→1.685 Å / Num. unique obs: 3568 / CC1/2: 0.774 / % possible all: 98.3

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Processing

Software
NameVersionClassification
MxCuBEdata collection
autoPROCdata processing
autoPROCdata scaling
autoPROCdata reduction
PHASERphasing
PHENIX1.14_3260refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BZ1,1FDH

1bz1

1fdh


Resolution: 1.66→52.946 Å / SU ML: 0.1848 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.6836 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2194 3552 4.89 %
Rwork0.1821 69079 -
obs0.1839 72631 98.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.56 Å2
Refinement stepCycle: LAST / Resolution: 1.66→52.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4533 0 0 565 5098
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00784666
X-RAY DIFFRACTIONf_angle_d0.95456393
X-RAY DIFFRACTIONf_chiral_restr0.0504700
X-RAY DIFFRACTIONf_plane_restr0.007792
X-RAY DIFFRACTIONf_dihedral_angle_d11.50872655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.680.2651500.25382696X-RAY DIFFRACTION98.31
1.68-1.70.33131330.25572704X-RAY DIFFRACTION97.39
1.7-1.730.29471450.24992705X-RAY DIFFRACTION98.68
1.73-1.760.2741180.22992730X-RAY DIFFRACTION97.47
1.76-1.780.26271520.22032690X-RAY DIFFRACTION98.68
1.78-1.820.26721570.21152734X-RAY DIFFRACTION98.5
1.82-1.850.26081620.212678X-RAY DIFFRACTION97.73
1.85-1.880.24471390.20252723X-RAY DIFFRACTION99.27
1.88-1.920.2361420.20762737X-RAY DIFFRACTION98.39
1.92-1.960.271300.20592754X-RAY DIFFRACTION98.06
1.96-2.010.26921300.20162752X-RAY DIFFRACTION99.04
2.01-2.060.24551460.19682738X-RAY DIFFRACTION99.31
2.06-2.120.241340.18952736X-RAY DIFFRACTION98.69
2.12-2.180.25841360.19112752X-RAY DIFFRACTION98.84
2.18-2.250.24721380.19222766X-RAY DIFFRACTION99.05
2.25-2.330.26751320.1922784X-RAY DIFFRACTION99.22
2.33-2.420.22871540.19842763X-RAY DIFFRACTION99.35
2.42-2.530.23961410.18982765X-RAY DIFFRACTION99.45
2.53-2.670.22381470.18942793X-RAY DIFFRACTION99.19
2.67-2.830.20411360.18632777X-RAY DIFFRACTION99.66
2.83-3.050.20771430.19222831X-RAY DIFFRACTION99.6
3.05-3.360.19021350.18522813X-RAY DIFFRACTION99.76
3.36-3.840.19041530.15832817X-RAY DIFFRACTION99.76
3.84-4.840.18731320.14722885X-RAY DIFFRACTION99.83
4.84-52.90.2111670.17322956X-RAY DIFFRACTION99

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