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- PDB-3onz: Human tetrameric hemoglobin: proximal nitrite ligand at beta -

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Basic information

Entry
Database: PDB / ID: 3onz
TitleHuman tetrameric hemoglobin: proximal nitrite ligand at beta
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / nitrite / human hemoglobin
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 / 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 / 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 / TOLUENE / NITRITE ION / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.087 Å
AuthorsYi, J. / Thormas, L.M. / Safo, M.K. / Musayev, F.N. / Richter-Addo, G.B.
CitationJournal: Biochemistry / Year: 2011
Title: Crystallographic Trapping of Heme Loss Intermediates during the Nitrite-Induced Degradation of Human Hemoglobin.
Authors: Yi, J. / Thomas, L.M. / Musayev, F.N. / Safo, M.K. / Richter-Addo, G.B.
History
DepositionAug 30, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 7, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_id / _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_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)32,73410
Polymers31,0412
Non-polymers1,6948
Water1,71195
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)65,46820
Polymers62,0814
Non-polymers3,38716
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area12000 Å2
ΔGint-65 kcal/mol
Surface area24610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.270, 53.270, 193.620
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-210-

HOH

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Components

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

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


Mass: 15150.353 Da / Num. of mol.: 1 / Fragment: Hemoglobin Chain A / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / Strain: Human / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / / Hemoglobin beta chain / Beta-globin / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 1 / Fragment: Hemoglobin Chain B / Source method: isolated from a natural source / Details: Blood / Source: (natural) Homo sapiens (human) / Strain: Human / References: UniProt: P68871

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Non-polymers , 4 types, 103 molecules

#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Chemical
ChemComp-MBN / TOLUENE / Toluene


Mass: 92.138 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.21 Å3/Da / Density % sol: 44.41 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 7.1
Details: sodium phospahte, potassium phosphate, toluene, nitrite, hemoglobin, pH 7.1, LIQUID DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Oct 11, 2007 / Details: Osmic
RadiationMonochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.09→46.7 Å / Num. all: 16567 / Num. obs: 16567 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 9.4 %
Reflection shellResolution: 2.09→2.2 Å / Redundancy: 9.4 % / Rmerge(I) obs: 0.405 / Mean I/σ(I) obs: 4.6 / % possible all: 90.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
PHENIX(phenix.refine: 1.6_289)refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1LJW

1ljw


Resolution: 2.087→26.635 Å / SU ML: 0.35 / Isotropic thermal model: isotropic / σ(F): 1.42 / Phase error: 26.47 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2796 856 5.18 %
Rwork0.2181 --
obs0.2212 16540 94.59 %
all-16567 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 71.087 Å2 / ksol: 0.37 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6842 Å20 Å20 Å2
2---0.6842 Å2-0 Å2
3---1.3683 Å2
Refinement stepCycle: LAST / Resolution: 2.087→26.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2076 0 120 95 2291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072261
X-RAY DIFFRACTIONf_angle_d1.063093
X-RAY DIFFRACTIONf_dihedral_angle_d18.428745
X-RAY DIFFRACTIONf_chiral_restr0.064334
X-RAY DIFFRACTIONf_plane_restr0.005384
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0871-2.21780.34471400.25892434X-RAY DIFFRACTION90
2.2178-2.38890.32461310.23642510X-RAY DIFFRACTION94
2.3889-2.62910.30891670.21952519X-RAY DIFFRACTION95
2.6291-3.00910.28791470.21652625X-RAY DIFFRACTION95
3.0091-3.78940.2391340.19662693X-RAY DIFFRACTION96
3.7894-26.63720.26181370.20632903X-RAY DIFFRACTION97

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