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- PDB-3ic0: Crystal Structure of liganded hemoglobin in complex with a potent... -

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Basic information

Entry
Database: PDB / ID: 3ic0
TitleCrystal Structure of liganded hemoglobin in complex with a potent antisickling agent, INN-298
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Heme protein / hemoglobin / Antisickling agents / Acetylation / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / Phosphoprotein / Polymorphism / Transport / Hypotensive agent / Pyruvate / S-nitrosylation / Vasoactive
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 / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
2-[(2-methoxy-5-methylphenoxy)methyl]pyridine / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsSafo, M.K. / Musayev, F.N. / Gandhi, A.K. / Jorge, P.
CitationJournal: To be Published
Title: Structural and in Vitro Chracterization of Pridyl Derivatives of Benzaldehydes: Highly Potent Antisickling Agents
Authors: Osheiza, A. / Mohini, G. / Ijoema, N. / Amit, K.G. / Faik, N.M. / Richmond, D.-D. / Toshio, A. / Martin, K.S.
History
DepositionJul 17, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Nov 27, 2019Group: Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)65,78418
Polymers62,0814
Non-polymers3,70314
Water7,476415
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12750 Å2
ΔGint-135 kcal/mol
Surface area22900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.978, 91.978, 143.942
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 / / Hemoglobin alpha chain / Alpha-globin


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 / / Hemoglobin beta chain / Beta-globin / LVV-hemorphin-7


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 , 5 types, 429 molecules

#3: Chemical
ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: O2
#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-B77 / 2-[(2-methoxy-5-methylphenoxy)methyl]pyridine


Mass: 229.274 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H15NO2
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 415 / Source method: isolated from a natural source / Formula: H2O

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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: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: 3.2 - 3.6 M Sulfate/phosphate precipitant, pH 6.5, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 8, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.8→38.75 Å / Num. obs: 65807 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Redundancy: 5.32 % / Biso Wilson estimate: 33 Å2 / Rmerge(I) obs: 0.059 / Χ2: 0.9 / Net I/σ(I): 14.6 / Scaling rejects: 37823
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.8-1.865.120.3464.53707664770.95100
1.86-1.945.040.3234.93756864930.99100
1.94-2.035.250.2885.33800765210.95100
2.03-2.135.280.2396.13831365400.94100
2.13-2.275.30.1887.43837865290.9399.9
2.27-2.445.330.1399.33885365520.91100
2.44-2.695.410.10411.83911265600.89100
2.69-3.085.460.06518.33980066190.84100
3.08-3.885.610.03928.94026366620.79100
3.88-38.755.380.02545.44055468540.8299.5

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Processing

Software
NameVersionClassificationNB
d*TREK9.2SSIdata processing
CNS1refinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1BBB

1bbb


Resolution: 1.8→27.78 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0.6 / Data cutoff high absF: 2426666 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23 3337 5.1 %RANDOM
Rwork0.201 ---
all0.211 65805 --
obs0.211 65805 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.444 Å2 / ksol: 0.357 e/Å3
Displacement parametersBiso max: 99.44 Å2 / Biso mean: 32.264 Å2 / Biso min: 12.93 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å22.3 Å20 Å2
2--1.14 Å20 Å2
3----2.29 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 1.8→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 258 415 5057
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.018
X-RAY DIFFRACTIONc_angle_deg2.1
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.56
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.88 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.38 398 4.9 %
Rwork0.365 7700 -
all-8098 -
obs--100 %

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