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- PDB-8fdm: Human Hemoglobin in Complex with Nitrosomethane -

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Basic information

Entry
Database: PDB / ID: 8fdm
TitleHuman Hemoglobin in Complex with Nitrosomethane
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / hemoglobin / nitrosomethane / sulfinic
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / 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
PROTOPORPHYRIN IX CONTAINING FE / TOLUENE / NITROSOMETHANE / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsPowell, S.M. / Richter-Addo, G.B. / Thomas, L.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: J.Inorg.Biochem. / Year: 2023
Title: Crystal structural investigations of heme protein derivatives resulting from reactions of aryl- and alkylhydroxylamines with human hemoglobin.
Authors: Powell, S.M. / Wang, B. / Herrera, V.E. / Prather, K.Y. / Nguyen, N.T. / Abucayon, E.G. / Thomas, L.M. / Safo, M.K. / Richter-Addo, G.B.
History
DepositionDec 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.details
Revision 1.2May 1, 2024Group: Database references / Category: citation
Item: _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)65,37718
Polymers62,0814
Non-polymers3,29614
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13420 Å2
ΔGint-96 kcal/mol
Surface area23230 Å2
Unit cell
Length a, b, c (Å)53.458, 53.458, 191.375
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Space group name HallP4w
Symmetry operation#1: x,y,z
#2: -y,x,z+1/4
#3: y,-x,z+3/4
#4: -x,-y,z+1/2

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

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


Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: Shr_HID2 / 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: 15890.198 Da / Num. of mol.: 2 / Fragment: Hb_alpha / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 6 types, 203 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MBN / TOLUENE


Mass: 92.138 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-NSM / NITROSOMETHANE


Mass: 45.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3NO
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 298 K / Method: batch mode / Details: 3.2 M sodium/potassium phosphate / PH range: 6.3-6.81

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-002 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Oct 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.91→46.67 Å / Num. obs: 40716 / % possible obs: 98.45 % / Redundancy: 1.9 % / Biso Wilson estimate: 27.2 Å2 / CC1/2: 0.996 / Net I/σ(I): 24.85
Reflection shellResolution: 1.91→1.98 Å / Num. unique obs: 3625 / CC1/2: 0.922

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-3000data collection
PHASERphasing
HKL-3000data scaling
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3P5Q

3p5q


Resolution: 1.91→46.67 Å / SU ML: 0.2545 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.9895
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2528 2073 5.09 %
Rwork0.196 38625 -
obs0.1989 40698 98.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.2 Å2
Refinement stepCycle: LAST / Resolution: 1.91→46.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4336 0 227 191 4754
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084742
X-RAY DIFFRACTIONf_angle_d0.96426496
X-RAY DIFFRACTIONf_chiral_restr0.0512702
X-RAY DIFFRACTIONf_plane_restr0.0075808
X-RAY DIFFRACTIONf_dihedral_angle_d13.1445642
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.950.37411170.27662013X-RAY DIFFRACTION78.22
1.95-20.30291240.22582571X-RAY DIFFRACTION98.07
2-2.060.28971430.22352656X-RAY DIFFRACTION99.79
2.06-2.120.32211410.21412568X-RAY DIFFRACTION99.89
2.12-2.190.28681390.2142617X-RAY DIFFRACTION100
2.19-2.260.25081520.21232611X-RAY DIFFRACTION100
2.26-2.350.27531510.21592616X-RAY DIFFRACTION99.93
2.35-2.460.28111180.20082627X-RAY DIFFRACTION99.96
2.46-2.590.26061560.20742615X-RAY DIFFRACTION99.93
2.59-2.750.29211240.21272638X-RAY DIFFRACTION99.93
2.75-2.970.25541500.20722648X-RAY DIFFRACTION99.93
2.97-3.260.24121650.20772560X-RAY DIFFRACTION99.78
3.26-3.740.21621260.1762654X-RAY DIFFRACTION99.53
3.74-4.70.2081330.16652602X-RAY DIFFRACTION99.2
4.71-46.670.25221340.1822629X-RAY DIFFRACTION98.93

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