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- PDB-7aet: Pressure wave-exposed human hemoglobin: probe only data (3500 ind... -

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Basic information

Entry
Database: PDB / ID: 7aet
TitlePressure wave-exposed human hemoglobin: probe only data (3500 indexed images)
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / XFEL / SFX / high pressure crystallography / hemoglobin
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / hemoglobin binding / organic acid binding / 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 / Late endosomal microautophagy / Heme signaling / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / 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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 2.53 Å
AuthorsBarends, T.R.M. / Schlichting, I.
CitationJournal: Nat Commun / Year: 2021
Title: Effect of X-ray free-electron laser-induced shockwaves on haemoglobin microcrystals delivered in a liquid jet.
Authors: Grunbein, M.L. / Gorel, A. / Foucar, L. / Carbajo, S. / Colocho, W. / Gilevich, S. / Hartmann, E. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Lewandowski, J. / ...Authors: Grunbein, M.L. / Gorel, A. / Foucar, L. / Carbajo, S. / Colocho, W. / Gilevich, S. / Hartmann, E. / Hilpert, M. / Hunter, M. / Kloos, M. / Koglin, J.E. / Lane, T.J. / Lewandowski, J. / Lutman, A. / Nass, K. / Nass Kovacs, G. / Roome, C.M. / Sheppard, J. / Shoeman, R.L. / Stricker, M. / van Driel, T. / Vetter, S. / Doak, R.B. / Boutet, S. / Aquila, A. / Decker, F.J. / Barends, T.R.M. / Stan, C.A. / Schlichting, I.
History
DepositionSep 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 17, 2021Provider: repository / Type: Initial release
Revision 1.1Apr 7, 2021Group: Database references / Category: citation / citation_author
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 1.2May 15, 2024Group: Data collection / Database references / Derived calculations
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Hemoglobin subunit alpha
BBB: Hemoglobin subunit beta
CCC: Hemoglobin subunit alpha
DDD: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,94812
Polymers61,3704
Non-polymers2,5788
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11330 Å2
ΔGint-114 kcal/mol
Surface area24540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.700, 158.100, 67.700
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14894.027 Da / Num. of mol.: 2 / 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: 15791.067 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 / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 38 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 49.35 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 3.2 M NaH2PO4/ 3.2 M K2HPO4 in a 2:1 ratio

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.743 Å
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jan 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.743 Å / Relative weight: 1
ReflectionResolution: 2.53→28.48 Å / Num. obs: 19339 / % possible obs: 99.9 % / Redundancy: 18.4 % / CC1/2: 0.702 / R split: 0.481 / Net I/σ(I): 2.1
Reflection shellResolution: 2.53→2.6 Å / Num. unique obs: 1011 / CC1/2: 0.233 / R split: 1.03

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
CrystFELdata reduction
CrystFELdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.53→28.06 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.879 / SU B: 24.395 / SU ML: 0.5 / Cross valid method: FREE R-VALUE / ESU R: 1.082 / ESU R Free: 0.356
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2883 1051 5.111 %
Rwork0.2276 19514 -
all0.231 --
obs-20565 97.183 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 44.782 Å2
Baniso -1Baniso -2Baniso -3
1--1.39 Å2-0 Å2-0 Å2
2---0.088 Å20 Å2
3---1.478 Å2
Refinement stepCycle: LAST / Resolution: 2.53→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 180 38 4550
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0134656
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174264
X-RAY DIFFRACTIONr_angle_refined_deg1.491.6956398
X-RAY DIFFRACTIONr_angle_other_deg1.1631.6129858
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4055564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96423.298188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.10415696
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.6391510
X-RAY DIFFRACTIONr_chiral_restr0.0620.2560
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025230
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02976
X-RAY DIFFRACTIONr_nbd_refined0.1820.2872
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1660.23363
X-RAY DIFFRACTIONr_nbtor_refined0.1470.22108
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21811
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.257
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1290.25
X-RAY DIFFRACTIONr_nbd_other0.1290.215
X-RAY DIFFRACTIONr_mcbond_it2.9044.672272
X-RAY DIFFRACTIONr_mcbond_other2.9064.672267
X-RAY DIFFRACTIONr_mcangle_it4.59772828
X-RAY DIFFRACTIONr_mcangle_other4.5967.0022829
X-RAY DIFFRACTIONr_scbond_it3.3134.9582384
X-RAY DIFFRACTIONr_scbond_other3.3134.9572382
X-RAY DIFFRACTIONr_scangle_it5.387.2743570
X-RAY DIFFRACTIONr_scangle_other5.387.2743570
X-RAY DIFFRACTIONr_lrange_it7.34453.2174968
X-RAY DIFFRACTIONr_lrange_other7.33953.2184966
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.53-2.5510.389230.345456X-RAY DIFFRACTION49.6888
2.551-2.620.359750.3431453X-RAY DIFFRACTION99.1564
2.62-2.6960.322701408X-RAY DIFFRACTION98.9953
2.696-2.7780.433770.321359X-RAY DIFFRACTION99.0345
2.778-2.8690.392680.3031326X-RAY DIFFRACTION99.3585
2.869-2.9690.328620.281287X-RAY DIFFRACTION98.8278
2.969-3.080.354650.2781245X-RAY DIFFRACTION99.393
3.08-3.2040.331660.2621195X-RAY DIFFRACTION99.7627
3.204-3.3450.316700.2591151X-RAY DIFFRACTION99.6735
3.345-3.5070.325610.2341115X-RAY DIFFRACTION99.5766
3.507-3.6940.289590.2221053X-RAY DIFFRACTION99.9101
3.694-3.9160.246580.2021003X-RAY DIFFRACTION99.9058
3.916-4.1820.223460.189969X-RAY DIFFRACTION100
4.182-4.5110.231380.175898X-RAY DIFFRACTION100
4.511-4.9330.221470.175818X-RAY DIFFRACTION100
4.933-5.5010.271340.183772X-RAY DIFFRACTION100
5.501-6.3240.295470.214663X-RAY DIFFRACTION100
6.324-7.6780.265440.2568X-RAY DIFFRACTION99.8369
7.678-10.5870.198220.175477X-RAY DIFFRACTION100
10.587-280.302190.229298X-RAY DIFFRACTION97.5385

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