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- PDB-1rq4: Crystallographic Analysis of the Interaction of Nitric Oxide with... -

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Basic information

Entry
Database: PDB / ID: 1rq4
TitleCrystallographic Analysis of the Interaction of Nitric Oxide with Quaternary-T Human Hemoglobin, HEMOGLOBIN EXPOSED TO NO UNDER AEROBIC CONDITIONS
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 / NITRIC OXIDE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.11 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_conn / struct_conn_type / struct_ref_seq_dif / 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.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)64,69912
Polymers62,1134
Non-polymers2,5868
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11940 Å2
ΔGint-121 kcal/mol
Surface area23690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.200, 100.400, 66.200
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: 15906.198 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: Chemical
ChemComp-NO / NITRIC OXIDE / Nitrogen monoxide


Mass: 30.006 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.67 %
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: Feb 8, 1999
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionHighest resolution: 2.11 Å / Num. obs: 36755 / % possible obs: 96.9 % / Redundancy: 6.3 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 8.1
Reflection shellResolution: 2.11→2.27 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.272 / Mean I/σ(I) obs: 1.5 / % possible all: 87.1
Reflection
*PLUS
Num. measured all: 232434
Reflection shell
*PLUS
% possible obs: 87.1 % / Num. unique obs: 6499 / Num. measured obs: 16661

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Processing

Software
NameVersionClassification
REFMAC5refinement
SDMSdata reduction
SDMSdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1RQ3

1rq3


Resolution: 2.11→10 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.731 / SU ML: 0.227 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.249 / ESU R Free: 0.2 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2414 3451 9.4 %matched to 1RQ3 data
Rwork0.19683 ---
obs0.20108 33380 95.55 %-
all-33380 --
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: 24.486 Å2
Baniso -1Baniso -2Baniso -3
1--1.77 Å20 Å20 Å2
2--3.03 Å20 Å2
3----1.26 Å2
Refinement stepCycle: LAST / Resolution: 2.11→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4386 0 180 164 4730
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.0394766
X-RAY DIFFRACTIONr_bond_other_d0.0010.024178
X-RAY DIFFRACTIONr_angle_refined_deg1.5052.0576436
X-RAY DIFFRACTIONr_angle_other_deg0.76739698
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.3953566
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.6515758
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.2700
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025164
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02890
X-RAY DIFFRACTIONr_nbd_refined0.2440.31204
X-RAY DIFFRACTIONr_nbd_other0.1970.33803
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2250.5200
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2640.54
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1110.38
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1420.311
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2070.59
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6841.52898
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.24224558
X-RAY DIFFRACTIONr_scbond_it1.9631860
X-RAY DIFFRACTIONr_scangle_it3.1234.51878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.11→2.154 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 24
Rwork0.312 1576
Software
*PLUS
Version: 5 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.241 / Rfactor Rwork: 0.197
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.021
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.51
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / Rfactor Rwork: 0.277

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