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- PDB-3d7o: Human hemoglobin, nitrogen dioxide anion modified -

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Basic information

Entry
Database: PDB / ID: 3d7o
TitleHuman hemoglobin, nitrogen dioxide anion modified
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Human Hemoglobin / Acetylation / Disease mutation / Glycation / Glycoprotein / Heme / Iron / Metal-binding / 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
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 / molecular replacement / Resolution: 1.8 Å
AuthorsYi, J. / Safo, M.K. / Richter-Addo, G.B.
CitationJournal: Biochemistry / Year: 2008
Title: The nitrite anion binds to human hemoglobin via the uncommon O-nitrito mode.
Authors: Yi, J. / Safo, M.K. / Richter-Addo, G.B.
History
DepositionMay 21, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_seq_id / _struct_conn.ptnr2_label_asym_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)32,4587
Polymers31,0412
Non-polymers1,4175
Water2,738152
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)64,91514
Polymers62,0814
Non-polymers2,83410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11950 Å2
ΔGint-102 kcal/mol
Surface area24020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.538, 53.538, 191.770
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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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 / 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.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 4 types, 157 molecules

#3: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


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


Mass: 92.138 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 152 / 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: 44.43 %
Crystal growTemperature: 295 K / Method: liquid diffusion / pH: 6.8
Details: Sodium phosphate, Potassium phosphate, Toluene, Hemoglobin, pH 6.8, LIQUID DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: May 16, 2008 / 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: 1.8→16.37 Å / Num. all: 26808 / Num. obs: 26808 / % possible obs: 99.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.74 % / Biso Wilson estimate: 36.6 Å2 / Rmerge(I) obs: 0.082 / Χ2: 0.96 / Net I/σ(I): 10.2 / Scaling rejects: 1568
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.457 / Mean I/σ(I) obs: 2.9 / Num. measured all: 10752 / Num. unique all: 2558 / Χ2: 1.16 / % possible all: 98.3

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.09 Å16.37 Å
Translation2.09 Å16.37 Å

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Processing

Software
NameVersionClassificationNB
d*TREK9.9Ddata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry 1IRD

1ird


Resolution: 1.8→16.37 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.01 / SU ML: 0.094 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.151 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1347 5 %RANDOM
Rwork0.206 ---
all0.237 26805 --
obs0.208 26803 99.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.993 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.1 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.8→16.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2217 0 99 152 2468
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0222391
X-RAY DIFFRACTIONr_angle_refined_deg1.5222.0623281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1935293
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.38923.97893
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.98615362
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.709156
X-RAY DIFFRACTIONr_chiral_restr0.1130.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021820
X-RAY DIFFRACTIONr_nbd_refined0.2180.21210
X-RAY DIFFRACTIONr_nbtor_refined0.2990.21625
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2140
X-RAY DIFFRACTIONr_metal_ion_refined0.0350.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3060.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.211
X-RAY DIFFRACTIONr_mcbond_it1.0111.51486
X-RAY DIFFRACTIONr_mcangle_it1.55122313
X-RAY DIFFRACTIONr_scbond_it2.38431033
X-RAY DIFFRACTIONr_scangle_it3.4774.5960
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.353 94 -
Rwork0.282 1810 -
all-1904 -
obs--97.74 %

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