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- PDB-7ud8: Crystal structure of carbon monoxy Hemoglobin in complex with 5HM... -

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Basic information

Entry
Database: PDB / ID: 7ud8
TitleCrystal structure of carbon monoxy Hemoglobin in complex with 5HMF at 1.8 Angstrom
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / hemoglobin / sickle cell disease / antisickling / NO release / oxygen equilibrium
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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 domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / (5-methylfuran-2-yl)methanol / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDonkor, A.K. / Musayev, F.N. / Safo, M.S.
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: Biomolecules / Year: 2022
Title: Design, Synthesis, and Antisickling Investigation of a Nitric Oxide-Releasing Prodrug of 5HMF for the Treatment of Sickle Cell Disease.
Authors: Alhashimi, R.T. / Ghatge, M.S. / Donkor, A.K. / Deshpande, T.M. / Anabaraonye, N. / Alramadhani, D. / Danso-Danquah, R. / Huang, B. / Zhang, Y. / Musayev, F.N. / Abdulmalik, O. / Safo, M.K.
History
DepositionMar 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 30, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 29, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 20, 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

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)65,42414
Polymers62,6064
Non-polymers2,81810
Water11,692649
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11560 Å2
ΔGint-106 kcal/mol
Surface area23550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.234, 92.234, 144.065
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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, 659 molecules

#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2 / Feature type: SUBJECT OF INVESTIGATION
#4: 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
#5: Chemical ChemComp-MW0 / (5-methylfuran-2-yl)methanol


Mass: 112.127 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O2
Details: The ligand MW0 is an aromatic aldehyde. The aldehyde moiety reacts with the N-terminal amine of Val1 of Hb forming a Schiff-base. That is C1 makes a double bond interaction with the amine ...Details: The ligand MW0 is an aromatic aldehyde. The aldehyde moiety reacts with the N-terminal amine of Val1 of Hb forming a Schiff-base. That is C1 makes a double bond interaction with the amine nitrogen of hemoglobin. The leaving group is water.
Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3.2-3.6M Sulfate/phosphate precipitant, pH 6.5, ferrous citrate

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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 15, 2019 / 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: 1.8→28.39 Å / Num. obs: 66309 / % possible obs: 100 % / Redundancy: 10.8 % / Biso Wilson estimate: 22.64 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.02 / Rrim(I) all: 0.065 / Net I/σ(I): 28.8 / Num. measured all: 716379 / Scaling rejects: 443
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
1.8-1.845.30.7962083638960.750.3710.882299.7
9-28.3910.70.02638659610.0060.021105.997.1

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Processing

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

3ic0


Resolution: 1.8→28.386 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2279 3361 5.08 %
Rwork0.1859 62737 -
obs0.188 66098 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 77.48 Å2 / Biso mean: 27.2803 Å2 / Biso min: 10.42 Å2
Refinement stepCycle: final / Resolution: 1.8→28.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 196 653 5233
Biso mean--24.63 35.42 -
Num. residues----574
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.82570.25551480.2376254199
1.8257-1.8530.29491270.2412593100
1.853-1.88190.29011150.2539261799
1.8819-1.91280.28571470.2668254099
1.9128-1.94570.35261340.25822590100
1.9457-1.98110.27611370.24232594100
1.9811-2.01920.23281200.20872616100
2.0192-2.06040.23531350.19792610100
2.0604-2.10520.25841330.19032607100
2.1052-2.15420.24511480.19182562100
2.1542-2.2080.2591590.2107255799
2.208-2.26770.26011540.2266255899
2.2677-2.33440.23131540.2028255698
2.3344-2.40970.23381320.17682622100
2.4097-2.49580.22361240.17442641100
2.4958-2.59560.19631390.17932601100
2.5956-2.71370.24521420.18372635100
2.7137-2.85660.2381580.18262597100
2.8566-3.03540.22081740.182576100
3.0354-3.26940.18961460.17852639100
3.2694-3.59790.21941590.16912647100
3.5979-4.11710.18211270.14552674100
4.1171-5.1820.19071060.16142744100
5.182-28.3860.23341430.19062820100

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