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- PDB-6xd9: Carbonmonoxy hemoglobin in complex with the antisickling agent 2-... -

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Basic information

Entry
Database: PDB / ID: 6xd9
TitleCarbonmonoxy hemoglobin in complex with the antisickling agent 2-hydroxy-6-((6-(hydroxymethyl)pyridin-2-yl)methoxy)benzaldehyde (VZHE039)
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / Aromatic aldehyde / Antisickling / Allosteric effector
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin 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 / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / 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 / blood microparticle / ficolin-1-rich granule lumen / 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 family profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Chem-V39 / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsPagare, P.P. / Safo, M.K. / Musayev, F.N.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)RO1MD009124 United States
National Institutes of Health/Office of the DirectorS10OD021756 United States
CitationJournal: Sci Rep / Year: 2020
Title: VZHE-039, a novel antisickling agent that prevents erythrocyte sickling under both hypoxic and anoxic conditions.
Authors: Abdulmalik, O. / Pagare, P.P. / Huang, B. / Xu, G.G. / Ghatge, M.S. / Xu, X. / Chen, Q. / Anabaraonye, N. / Musayev, F.N. / Omar, A.M. / Venitz, J. / Zhang, Y. / Safo, M.K.
History
DepositionJun 10, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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
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)65,15014
Polymers62,0814
Non-polymers3,06910
Water9,332518
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11780 Å2
ΔGint-118 kcal/mol
Surface area23240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.778, 82.628, 104.997
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: 15150.353 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: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 528 molecules

#3: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#4: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical ChemComp-V39 / 3-{[6-(hydroxymethyl)pyridin-2-yl]methoxy}-2-methylphenol


Mass: 245.274 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 518 / 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: 2.19 Å3/Da / Density % sol: 43.92 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 7.4 / Details: 25% PEG 6000, 0.1M HEPES

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å
DetectorType: DECTRIS EIGER R 4M / Detector: PIXEL / Date: Sep 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5419 Å / Relative weight: 1
ReflectionResolution: 2.1→29.343 Å / Num. obs: 31379 / % possible obs: 96.3 % / Redundancy: 4.62 % / Biso Wilson estimate: 29.99 Å2 / Rmerge(I) obs: 0.068 / Rrim(I) all: 0.076 / Χ2: 1.02 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsRrim(I) allΧ2% possible all
2.1-2.184.470.3423.930670.3871.2495.4
2.18-2.264.530.3084.230520.3471.2295.4
2.26-2.374.530.254530520.2861.1695.2
2.37-2.494.540.2145.930730.2411.1495.6
2.49-2.654.510.1836.830940.2071.1496
2.65-2.854.490.1348.931140.1511.0695.9
2.85-3.144.570.09411.631300.1060.9796.5
3.14-3.594.680.06317.232070.070.8897.7
3.59-4.524.960.0412532700.0460.7799.1
4.52-29.344.850.0313033200.0350.7796

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystalClear2data collection
CrystalClear2data scaling
d*TREKdata reduction
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BBB

1bbb


Resolution: 2.1→29.343 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2582 1593 5.08 %
Rwork0.1972 29757 -
obs0.2002 31350 96.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 68.96 Å2 / Biso mean: 31.0156 Å2 / Biso min: 16.99 Å2
Refinement stepCycle: final / Resolution: 2.1→29.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 216 525 5125
Biso mean--27.96 35.3 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034752
X-RAY DIFFRACTIONf_angle_d0.6966500
X-RAY DIFFRACTIONf_chiral_restr0.025700
X-RAY DIFFRACTIONf_plane_restr0.004810
X-RAY DIFFRACTIONf_dihedral_angle_d12.511614
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1-2.16780.28921520.2427262695
2.1678-2.24520.3231420.244263395
2.2452-2.33510.30291430.238261995
2.3351-2.44130.27331300.2313266696
2.4413-2.570.31881430.2279266096
2.57-2.73090.27941400.228268896
2.7309-2.94160.25871450.2235268296
2.9416-3.23720.29731340.2169270897
3.2372-3.70490.23151510.187279898
3.7049-4.66470.22261580.1562281999
4.6647-29.3430.23741550.1701285896

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