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- PDB-8egi: X-ray structure of carbonmonoxy hemoglobin in complex with VZHE039-NO -

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Basic information

Entry
Database: PDB / ID: 8egi
TitleX-ray structure of carbonmonoxy hemoglobin in complex with VZHE039-NO
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / sickle cell disease / antisickling / nitric oxide / oxygen equilibrium curve
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / 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 / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / blood microparticle / ficolin-1-rich granule lumen / iron ion binding / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-VZN / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsDonkor, A.K. / Musayev, F.N. / Safo, M.K.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)R01MD009124 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)R61HL156158 United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR)S10OD021756 United States
CitationJournal: Molecules / Year: 2022
Title: Design, Synthesis, and Investigation of Novel Nitric Oxide (NO)-Releasing Aromatic Aldehydes as Drug Candidates for the Treatment of Sickle Cell Disease.
Authors: Huang, B. / Ghatge, M.S. / Donkor, A.K. / Musayev, F.N. / Deshpande, T.M. / Al-Awadh, M. / Alhashimi, R.T. / Zhu, H. / Omar, A.M. / Telen, M.J. / Zhang, Y. / McMahon, T.J. / Abdulmalik, O. / Safo, M.K.
History
DepositionSep 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 13, 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

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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)65,76414
Polymers62,6064
Non-polymers3,15910
Water7,999444
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11980 Å2
ΔGint-114 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.893, 82.562, 105.240
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: 15281.550 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Homo sapiens (human) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 16021.396 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 454 molecules

#3: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-VZN / {6-[(3-hydroxy-2-methylphenoxy)methyl]pyridin-2-yl}methyl nitrate


Mass: 290.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H14N2O5 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / 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: 2.1 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 30 mg/dL of CO-ligated Hb crystallized using 10-20% PEG 6000, 100 mM Hepes, pH 7.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5406 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Apr 22, 2021 / Details: VariMax TM-VHF Arc)Sec Confocal Optical System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5406 Å / Relative weight: 1
ReflectionResolution: 2.3→28.86 Å / Num. obs: 25048 / % possible obs: 99.9 % / Redundancy: 8.1 % / Biso Wilson estimate: 23.92 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.039 / Rrim(I) all: 0.113 / Net I/σ(I): 15.7 / Num. measured all: 202614 / Scaling rejects: 92
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.3-2.388.30.4591987024050.9430.1690.495.199.8
8.91-28.867.10.03434644860.9990.0130.0364997.2

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.27data extraction
CrysalisPro41.64.69adata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IC0

3ic0


Resolution: 2.3→28.858 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2512 1174 4.7 %
Rwork0.184 23813 -
obs0.187 24987 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 73.1 Å2 / Biso mean: 25.9502 Å2 / Biso min: 9.74 Å2
Refinement stepCycle: final / Resolution: 2.3→28.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 222 446 5052
Biso mean--22.97 31.22 -
Num. residues----574
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork
2.3-2.40460.27421580.19192905
2.4046-2.53130.2911380.20372933
2.5313-2.68980.29041550.19382937
2.6898-2.89730.27371380.22952
2.8973-3.18860.25321390.19912960
3.1886-3.64920.23891470.18032966
3.6492-4.59460.23371340.15933031
4.5946-28.8580.22911650.18273129

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