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- PDB-4ni0: Quaternary R3 CO-liganded hemoglobin structure in complex with a ... -

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Basic information

Entry
Database: PDB / ID: 4ni0
TitleQuaternary R3 CO-liganded hemoglobin structure in complex with a thiol containing compound
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / allosteric / tetramer / relaxed state / Tense state / globin fold / Red blood cell
Function / homology
Function and homology information


cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin binding / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / 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 / Erythrocytes take up oxygen and release carbon dioxide / response to hydrogen peroxide / 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 / 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
Chem-2P3 / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / TOLUENE / PHOSPHATE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.15 Å
AuthorsSafo, M.K. / Meadows, J. / Ko, T.-P. / Nakagawa, A. / Zapol, W.
CitationJournal: Acs Chem.Biol. / Year: 2014
Title: Identification of a Small Molecule that Increases Hemoglobin Oxygen Affinity and Reduces SS Erythrocyte Sickling.
Authors: Nakagawa, A. / Lui, F.E. / Wassaf, D. / Yefidoff-Freedman, R. / Casalena, D. / Palmer, M.A. / Meadows, J. / Mozzarelli, A. / Ronda, L. / Abdulmalik, O. / Bloch, K.D. / Safo, M.K. / Zapol, W.M.
History
DepositionNov 5, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 29, 2014Group: Database references
Revision 1.2Sep 20, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,83216
Polymers31,0412
Non-polymers2,79114
Water2,846158
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,66432
Polymers62,0814
Non-polymers5,58328
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/41
Buried area7270 Å2
ΔGint-26 kcal/mol
Surface area24330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.0636, 62.0636, 173.8816
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

21A-302-

HOH

31B-301-

HOH

41B-302-

HOH

51B-303-

HOH

61B-311-

HOH

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Components

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Hemoglobin subunit ... , 2 types, 2 molecules AB

#1: Protein Hemoglobin subunit alpha / / Alpha-globin / Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 1 / 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 / LVV-hemorphin-7 / Spinorphin


Mass: 15890.198 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 6 types, 172 molecules

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


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#5: Chemical
ChemComp-2P3 / 5-[(2S)-2,3-dihydro-1,4-benzodioxin-2-yl]-2,4-dihydro-3H-1,2,4-triazole-3-thione


Mass: 235.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H9N3O2S
#6: Chemical ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C7H8
#7: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 158 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsLIGAND 2P3 AND 2JX ARE RACEMIC MIXTURES OF COMPOUND 3-(2,3-DIHYDROBENZO[1,4]DIOXIN-2-YL)-3H-1,2,4- ...LIGAND 2P3 AND 2JX ARE RACEMIC MIXTURES OF COMPOUND 3-(2,3-DIHYDROBENZO[1,4]DIOXIN-2-YL)-3H-1,2,4-TRIAZOLE-5-THIOL. ONLY 2P3 ISOMERS WERE MODELED IN THIS STRUCTURE.

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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: 54.4 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.8
Details: 20-30mg/mL protein, 3.0-3.4 M Sodium/potassium phosphate, pH 6.8, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 16, 2013
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.15→29.2 Å / Num. all: 19122 / Num. obs: 19122 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.8 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 14.9
Reflection shellResolution: 2.15→2.18 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.4 / % possible all: 97.9

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Processing

Software
NameClassification
CrystalCleardata collection
CNSrefinement
d*TREKdata reduction
d*TREKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1YZI

1yzi


Resolution: 2.15→18.59 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2325812.5 / 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
Rfree0.259 979 5.1 %RANDOM
Rwork0.228 ---
all0.234 19071 --
obs0.228 19071 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 84.9353 Å2 / ksol: 0.380658 e/Å3
Displacement parametersBiso mean: 47.2 Å2
Baniso -1Baniso -2Baniso -3
1-2.84 Å20 Å20 Å2
2--2.84 Å20 Å2
3----5.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.32 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.46 Å
Refinement stepCycle: LAST / Resolution: 2.15→18.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 190 158 2540
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg2
X-RAY DIFFRACTIONc_dihedral_angle_d18.9
X-RAY DIFFRACTIONc_improper_angle_d1.39
Refine LS restraints NCSNCS model details: NONE
LS refinement shellResolution: 2.15→2.23 Å / Rfactor Rfree error: 0.038 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.376 99 5.4 %
Rwork0.392 1744 -
obs--97.9 %

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