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- PDB-7vld: Oxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation -

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Basic information

Entry
Database: PDB / ID: 7vld
TitleOxy-deoxy intermediate of V2 hemoglobin at 69% oxygen saturation
Components(Extracellular ...) x 4
KeywordsOXYGEN TRANSPORT / allostery / structural transition / giant hemoglobin
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / response to hypoxia / iron ion binding / heme binding / extracellular region
Similarity search - Function
Casein alpha/beta, conserved site / Caseins alpha/beta signature. / Globin, extracellular / Erythrocruorin / : / Myoglobin-like, M family globin domain / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Extracellular globin / Extracellular globin / Extracellular globin / Extracellular globin
Similarity search - Component
Biological speciesLamellibrachia satsuma (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsNumoto, N. / Onoda, S. / 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: Biophys Physicobio. / Year: 2022
Title: Structures of oxygen dissociation intermediates of 400 kDa V2 hemoglobin provide coarse snapshots of the protein allostery.
Authors: Numoto, N. / Onoda, S. / Kawano, Y. / Okumura, H. / Baba, S. / Fukumori, Y. / Miki, K. / Ito, N.
History
DepositionOct 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 20, 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 A1 globin
B: Extracellular A2 globin
C: Extracellular B2 globin
D: Extracellular B1 globin
E: Extracellular A1 globin
F: Extracellular A2 globin
G: Extracellular B2 globin
H: Extracellular B1 globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,14028
Polymers130,1388
Non-polymers6,00320
Water14,376798
1
A: Extracellular A1 globin
B: Extracellular A2 globin
C: Extracellular B2 globin
D: Extracellular B1 globin
E: Extracellular A1 globin
F: Extracellular A2 globin
G: Extracellular B2 globin
H: Extracellular B1 globin
hetero molecules

A: Extracellular A1 globin
B: Extracellular A2 globin
C: Extracellular B2 globin
D: Extracellular B1 globin
E: Extracellular A1 globin
F: Extracellular A2 globin
G: Extracellular B2 globin
H: Extracellular B1 globin
hetero molecules

A: Extracellular A1 globin
B: Extracellular A2 globin
C: Extracellular B2 globin
D: Extracellular B1 globin
E: Extracellular A1 globin
F: Extracellular A2 globin
G: Extracellular B2 globin
H: Extracellular B1 globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)408,42184
Polymers390,41324
Non-polymers18,00860
Water43224
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area94240 Å2
ΔGint-759 kcal/mol
Surface area125770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.263, 110.263, 196.968
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

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Extracellular ... , 4 types, 8 molecules AEBFCGDH

#1: Protein Extracellular A1 globin


Mass: 16368.704 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BBU7
#2: Protein Extracellular A2 globin


Mass: 15951.922 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BBR6
#3: Protein Extracellular B2 globin


Mass: 16519.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BCU7
#4: Protein Extracellular B1 globin


Mass: 16228.627 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Lamellibrachia satsuma (invertebrata) / References: UniProt: S0BAP9

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Sugars , 1 types, 2 molecules

#5: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 816 molecules

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


Mass: 31.999 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.66 Å3/Da / Density % sol: 53.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 14-17% (w/v) PEG 3350, 100mM HEPES-NaOH pH 7.5

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 12, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 77995 / % possible obs: 98.9 % / Redundancy: 10.1 % / Biso Wilson estimate: 37.89 Å2 / CC1/2: 0.999 / Rsym value: 0.088 / Net I/σ(I): 17.8
Reflection shellResolution: 2.1→2.23 Å / Redundancy: 5.3 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 62700 / CC1/2: 0.529 / Rsym value: 1.05 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WCT

3wct


Resolution: 2.1→49.24 Å / SU ML: 0.2881 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.4684 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2212 3914 5.02 %
Rwork0.1898 74076 -
obs0.1913 77990 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 39.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→49.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9114 0 410 798 10322
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00329820
X-RAY DIFFRACTIONf_angle_d0.605313412
X-RAY DIFFRACTIONf_chiral_restr0.03711400
X-RAY DIFFRACTIONf_plane_restr0.00291714
X-RAY DIFFRACTIONf_dihedral_angle_d18.42915658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.130.32651180.29742359X-RAY DIFFRACTION87.4
2.13-2.150.31111300.27122420X-RAY DIFFRACTION91.69
2.15-2.180.29581340.26652494X-RAY DIFFRACTION94.94
2.18-2.210.32431400.25322666X-RAY DIFFRACTION97.36
2.21-2.240.32741400.25382616X-RAY DIFFRACTION99.35
2.24-2.280.30561430.24912675X-RAY DIFFRACTION100
2.28-2.310.29191440.23872668X-RAY DIFFRACTION100
2.31-2.350.26111410.22682675X-RAY DIFFRACTION100
2.35-2.390.29731360.21622653X-RAY DIFFRACTION100
2.39-2.430.2651430.20732659X-RAY DIFFRACTION100
2.43-2.480.25541450.20612681X-RAY DIFFRACTION100
2.48-2.530.26861240.20562665X-RAY DIFFRACTION100
2.53-2.590.22751380.20252677X-RAY DIFFRACTION100
2.59-2.650.24091390.19942678X-RAY DIFFRACTION100
2.65-2.710.2391410.19892657X-RAY DIFFRACTION100
2.71-2.790.2591300.19952703X-RAY DIFFRACTION100
2.79-2.870.24871510.19952632X-RAY DIFFRACTION99.96
2.87-2.960.24541370.19482697X-RAY DIFFRACTION100
2.96-3.070.24631560.19892665X-RAY DIFFRACTION100
3.07-3.190.24411500.19692646X-RAY DIFFRACTION100
3.19-3.330.22741590.19772669X-RAY DIFFRACTION100
3.33-3.510.23121310.18492672X-RAY DIFFRACTION100
3.51-3.730.18741470.17362666X-RAY DIFFRACTION100
3.73-4.020.20291300.16732693X-RAY DIFFRACTION100
4.02-4.420.18671460.1622713X-RAY DIFFRACTION100
4.42-5.060.16631370.16142654X-RAY DIFFRACTION100
5.06-6.370.21391400.18762699X-RAY DIFFRACTION100
6.37-49.240.16461440.16762724X-RAY DIFFRACTION99.9

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