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- PDB-9rxg: Work experience structure of Bovine Hemoglobin, collected at room... -

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Basic information

Entry
Database: PDB / ID: 9rxg
TitleWork experience structure of Bovine Hemoglobin, collected at room temperature.
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Room temperature / multi-crystal
Function / homology
Function and homology information


Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex ...Scavenging of heme from plasma / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / Cytoprotection by HMOX1 / Neutrophil degranulation / hemoglobin alpha binding / cellular oxidant detoxification / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen carrier activity / hydrogen peroxide catabolic process / oxygen binding / iron ion binding / heme binding / metal ion binding
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 alpha / Hemoglobin subunit beta
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsSandy, J. / Balagan, P. / Inyang, M. / Kibelkyte, I.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Diamond Light Source United Kingdom
CitationJournal: To Be Published
Title: Work experience structure of Bovine Hemoglobin, collected at room temperature.
Authors: Sandy, J. / Balagan, P. / Inyang, M. / Kibelkyte, I.
History
DepositionJul 11, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2025Provider: repository / Type: Initial release

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2618
Polymers61,7954
Non-polymers2,4664
Water32418
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.774, 79.118, 109.856
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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


Mass: 14919.978 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P01966
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15977.382 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / References: UniProt: P02070, quinol-cytochrome-c reductase
#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.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.3 Å3/Da / Density % sol: 46.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 0.1M Bis Tris Propane pH 6.7 28% PEG 3350 0.2M NaCl 0.2M KCl

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: VMXi / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER2 X 4M / Detector: PIXEL / Date: Jul 3, 2025
RadiationMonochromator: Double Multilayer Monochromator (DMM) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 2.62→64.77 Å / Num. obs: 17609 / % possible obs: 100 % / Redundancy: 73 % / Biso Wilson estimate: 55.11 Å2 / CC1/2: 1 / Net I/σ(I): 6.7
Reflection shellResolution: 2.62→2.7 Å / Num. unique obs: 1421 / CC1/2: 0.5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→64.2 Å / SU ML: 0.3091 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9935
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.233 1667 9.52 %
Rwork0.19 15844 -
obs0.1941 17511 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.87 Å2
Refinement stepCycle: LAST / Resolution: 2.62→64.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4313 0 172 18 4503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00444625
X-RAY DIFFRACTIONf_angle_d0.70456331
X-RAY DIFFRACTIONf_chiral_restr0.0406686
X-RAY DIFFRACTIONf_plane_restr0.0036791
X-RAY DIFFRACTIONf_dihedral_angle_d17.46411578
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.70.36111280.32751293X-RAY DIFFRACTION99.09
2.7-2.780.29151260.29731299X-RAY DIFFRACTION99.3
2.78-2.880.32611430.29131279X-RAY DIFFRACTION99.44
2.88-30.31261290.28491313X-RAY DIFFRACTION99.59
3-3.140.32671480.25281289X-RAY DIFFRACTION99.93
3.14-3.30.24331320.22731316X-RAY DIFFRACTION100
3.3-3.510.28051440.20951289X-RAY DIFFRACTION99.65
3.51-3.780.24831450.18861325X-RAY DIFFRACTION99.8
3.78-4.160.21921470.15581315X-RAY DIFFRACTION99.93
4.16-4.760.18241280.14331343X-RAY DIFFRACTION100
4.76-60.20721350.16921369X-RAY DIFFRACTION100
6-64.20.17711620.14491414X-RAY DIFFRACTION99.81

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