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- PDB-1rq3: Crystallographic Analysis of the Interaction of Nitric Oxide with... -

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Basic information

Entry
Database: PDB / ID: 1rq3
TitleCrystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Deoxyhemoglobin, Deoxyhemoglobin
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / globin / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / haptoglobin-hemoglobin complex / 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 / carbon dioxide transport / response to hydrogen peroxide / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / regulation of blood pressure / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / metal ion binding / membrane / cytosol
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsChan, N.L. / Kavanaugh, J.S. / Rogers, P.H. / Arnone, A.
CitationJournal: Biochemistry / Year: 2004
Title: Crystallographic analysis of the interaction of nitric oxide with quaternary-T human hemoglobin.
Authors: Chan, N.L. / Kavanaugh, J.S. / Rogers, P.H. / Arnone, A.
History
DepositionDec 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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 alpha chain
B: Hemoglobin beta chain
C: Hemoglobin alpha chain
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11290 Å2
ΔGint-106 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.000, 99.300, 66.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P69905
#2: Protein Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Tissue: blood / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.56 Å3/Da / Density % sol: 51.93 %
Crystal growpH: 7 / Details: pH 7.0
Crystal grow
*PLUS
Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlhuman hemoglobin11pH7.0
210 mMpotassium phosphate11
3100 mM11KCl
410-12 %PEG600011
53 mMsodium dithionite11

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: SDMS / Detector: AREA DETECTOR / Date: May 8, 1990
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 1.91 Å / Num. obs: 47999 / % possible obs: 95.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 23.2
Reflection shellResolution: 1.91→2.05 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.105 / Mean I/σ(I) obs: 2.9 / % possible all: 78.1

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Processing

Software
NameVersionClassification
REFMAC5refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1HBB

1hbb


Resolution: 1.91→10 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.353 / SU ML: 0.206 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.148 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19838 4832 10.1 %RANDOM
Rwork0.16727 ---
all-43149 --
obs-43149 94.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å20 Å2
2--1.59 Å20 Å2
3----1.16 Å2
Refinement stepCycle: LAST / Resolution: 1.91→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 172 175 4731
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0214700
X-RAY DIFFRACTIONr_bond_other_d0.0010.024182
X-RAY DIFFRACTIONr_angle_refined_deg1.862.0566446
X-RAY DIFFRACTIONr_angle_other_deg0.82439706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.8313570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.78915761
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1140.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025192
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02894
X-RAY DIFFRACTIONr_nbd_refined0.2360.31137
X-RAY DIFFRACTIONr_nbd_other0.1860.33829
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.5158
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0910.52
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2320.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3280.318
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it1.0721.52858
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.06424570
X-RAY DIFFRACTIONr_scbond_it3.15931842
X-RAY DIFFRACTIONr_scangle_it5.0744.51876
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.91→1.938 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.248 81
Rwork0.242 875

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