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- PDB-7e98: Oxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen ... -

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Basic information

Entry
Database: PDB / ID: 7.0E+98
TitleOxy-deoxy intermediate of 400 kDa giant hemoglobin at 21% oxygen saturation
Components
  • (Extracellular giant hemoglobin major globin subunit ...) x 3
  • Giant hemoglobin B1b globin chain
KeywordsOXYGEN TRANSPORT / allostery / structural change / microspectrometry / crystal processing.
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / extracellular region / metal ion binding
Similarity search - Function
Globin, extracellular / Erythrocruorin / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Giant hemoglobin B1b globin chain / Extracellular giant hemoglobin major globin subunit A2 / Extracellular giant hemoglobin major globin subunit B2 / Extracellular giant hemoglobin major globin subunit A1
Similarity search - Component
Biological speciesOligobrachia mashikoi (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsNumoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)25870200 Japan
Japan Society for the Promotion of Science (JSPS)15K20971 Japan
CitationJournal: Iucrj / Year: 2021
Title: Coarse snapshots of oxygen-dissociation intermediates of a giant hemoglobin elucidated by determining the oxygen saturation in individual subunits in the crystalline state.
Authors: Numoto, N. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N.
History
DepositionMar 3, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Giant hemoglobin B1b globin chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,51713
Polymers60,8314
Non-polymers2,6869
Water6,089338
1
A: Extracellular giant hemoglobin major globin subunit A1
B: Extracellular giant hemoglobin major globin subunit A2
C: Extracellular giant hemoglobin major globin subunit B2
D: Giant hemoglobin B1b globin chain
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)381,10078
Polymers364,98424
Non-polymers16,11654
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555y,x,-z1
crystal symmetry operation5_555x-y,-y,-z1
crystal symmetry operation6_555-x,-x+y,-z1
Buried area92310 Å2
ΔGint-727 kcal/mol
Surface area110120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.245, 112.245, 271.388
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11A-343-

HOH

21A-366-

HOH

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Components

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Extracellular giant hemoglobin major globin subunit ... , 3 types, 3 molecules ABC

#1: Protein Extracellular giant hemoglobin major globin subunit A1 / Major globin chain b


Mass: 15188.894 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M419
#2: Protein Extracellular giant hemoglobin major globin subunit A2 / Major globin chain a5


Mass: 15327.087 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M413
#3: Protein Extracellular giant hemoglobin major globin subunit B2 / Major globin chain c


Mass: 15621.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: Q7M418

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Protein , 1 types, 1 molecules D

#4: Protein Giant hemoglobin B1b globin chain


Mass: 14693.341 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oligobrachia mashikoi (invertebrata) / References: UniProt: B1Q3G1

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Non-polymers , 4 types, 347 molecules

#5: 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
#6: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 338 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.7 Å3/Da / Density % sol: 54.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 11-12 % (w/v) polyethylene glycol (PEG) 10,000, 10 mM CaCl2, 200 mM Tris-HCl pH 8.0

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1.1 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Nov 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 33753 / % possible obs: 99.7 % / Redundancy: 10.3 % / Biso Wilson estimate: 36.6 Å2 / CC1/2: 0.997 / Rsym value: 0.19 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.33 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 5320 / CC1/2: 0.666 / Rsym value: 1.9

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHASERphasing
XDSdata scaling
XDSdata processing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2ZFO

2zfo


Resolution: 2.2→47.84 Å / SU ML: 0.2763 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.5921 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2193 1686 5 %
Rwork0.1875 32046 -
obs0.1891 33732 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4257 0 186 338 4781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00264556
X-RAY DIFFRACTIONf_angle_d0.67436239
X-RAY DIFFRACTIONf_chiral_restr0.0332660
X-RAY DIFFRACTIONf_plane_restr0.0027814
X-RAY DIFFRACTIONf_dihedral_angle_d15.17542611
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.260.31631340.29922567X-RAY DIFFRACTION97.54
2.26-2.340.29081620.27682620X-RAY DIFFRACTION99.64
2.34-2.420.30741350.24562652X-RAY DIFFRACTION99.86
2.42-2.520.27541410.24232625X-RAY DIFFRACTION99.64
2.52-2.630.26811450.22822650X-RAY DIFFRACTION99.89
2.63-2.770.26441080.2082700X-RAY DIFFRACTION99.75
2.77-2.940.23321340.20582656X-RAY DIFFRACTION99.93
2.94-3.170.26481320.20022683X-RAY DIFFRACTION99.96
3.17-3.490.23041570.18562661X-RAY DIFFRACTION99.96
3.49-3.990.19571470.15632692X-RAY DIFFRACTION100
3.99-5.030.16291430.14722715X-RAY DIFFRACTION99.97
5.03-47.840.17821480.16482825X-RAY DIFFRACTION99.7

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