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- PDB-5kdq: Deoxyhemoglobin in Complex with an Aryloxyalkanoic acid -

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Basic information

Entry
Database: PDB / ID: 5kdq
TitleDeoxyhemoglobin in Complex with an Aryloxyalkanoic acid
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / sickle cell disease / allosteric effector / aryloxyalkanoic
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid 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 / 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 / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Chem-KOH / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsAhmed, M.H. / Omar, A.M. / Safo, M.K.
Funding support Saudi Arabia, United States, 4items
OrganizationGrant numberCountry
MAARIFAHBIO1253-03-10 Saudi Arabia
National Institutes of Health/National Institute on Minority Health and Health Disparities (NIH/NIMHD)MD009124 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)K01HL103186 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA16059 United States
CitationJournal: Molecules / Year: 2016
Title: Aryloxyalkanoic Acids as Non-Covalent Modifiers of the Allosteric Properties of Hemoglobin.
Authors: Omar, A.M. / Mahran, M.A. / Ghatge, M.S. / Bamane, F.H. / Ahmed, M.H. / El-Araby, M.E. / Abdulmalik, O. / Safo, M.K.
History
DepositionJun 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 20, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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)65,00411
Polymers62,0814
Non-polymers2,9237
Water6,666370
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12040 Å2
ΔGint-114 kcal/mol
Surface area23060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.222, 80.830, 53.397
Angle α, β, γ (deg.)90.00, 80.77, 90.00
Int Tables number4
Space group name H-MP1211

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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 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: 15890.198 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, 377 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-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-KOH / 3-[2-chloranyl-4-(1~{H}-imidazol-2-yl)phenoxy]propanoic acid


Mass: 266.680 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H11ClN2O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 370 / 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: 2.13 Å3/Da / Density % sol: 42.39 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.5
Details: 3.2 M Sulfate/phosphate precipitant, pH 6.8, LIQUID DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: Cu FINE FOCUS / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.15→29.64 Å / Num. obs: 27383 / % possible obs: 96.2 % / Redundancy: 6.75 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 21
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 6.73 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 8.4 / % possible all: 94.1

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Processing

Software
NameVersionClassification
PHENIX1.6.4_486refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIX1.6.4_486phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 2DN2

2dn2


Resolution: 2.15→29.64 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.55
RfactorNum. reflection% reflectionSelection details
Rfree0.2571 1389 5.08 %0.05
Rwork0.1924 ---
obs0.1957 27358 96.08 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Bsol: 43.074 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.4449 Å20 Å2-2.8152 Å2
2--10.4925 Å20 Å2
3----4.0476 Å2
Refinement stepCycle: LAST / Resolution: 2.15→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 200 370 4954
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074731
X-RAY DIFFRACTIONf_angle_d1.2846491
X-RAY DIFFRACTIONf_dihedral_angle_d14.2351606
X-RAY DIFFRACTIONf_chiral_restr0.065700
X-RAY DIFFRACTIONf_plane_restr0.005809
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.15-2.22680.35691360.24732521X-RAY DIFFRACTION94
2.2268-2.3160.34471300.23682550X-RAY DIFFRACTION94
2.316-2.42130.30561560.22852525X-RAY DIFFRACTION95
2.4213-2.54890.31211190.2122573X-RAY DIFFRACTION95
2.5489-2.70850.28251240.21642590X-RAY DIFFRACTION96
2.7085-2.91750.31511200.20982621X-RAY DIFFRACTION96
2.9175-3.21080.26931380.21072597X-RAY DIFFRACTION97
3.2108-3.67460.23641530.18462642X-RAY DIFFRACTION97
3.6746-4.62680.19531610.15412639X-RAY DIFFRACTION98
4.6268-29.64280.23821520.17382711X-RAY DIFFRACTION98

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