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- PDB-1jy7: THE STRUCTURE OF HUMAN METHEMOGLOBIN. THE VARIATION OF A THEME -

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Basic information

Entry
Database: PDB / ID: 1jy7
TitleTHE STRUCTURE OF HUMAN METHEMOGLOBIN. THE VARIATION OF A THEME
Components
  • Hemoglobin alpha chain
  • Hemoglobin beta chain
KeywordsOXYGEN STORAGE/TRANSPORT / HUMAN METHEMOGLOBIN / OXYGEN TRANSPORT / 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 / oxygen carrier activity / hydrogen peroxide catabolic process / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Heme signaling / Late endosomal microautophagy / Cytoprotection by HMOX1 / oxygen binding / platelet aggregation / 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 / 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: 3.2 Å
AuthorsBiswal, B.K. / Vijayan, M.
Citation
Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Structures of human oxy- and deoxyhaemoglobin at different levels of humidity: variability in the T state.
Authors: Biswal, B.K. / Vijayan, M.
#1: Journal: Curr.Sci. / Year: 2001
Title: Structure of human methaemoglobin: The variation of a theme
Authors: Biswal, B.K. / Vijayan, M.
#2: Journal: J.Mol.Biol. / Year: 1983
Title: Structure of human oxyhaemoglobin at 2.1 A resolution
Authors: Shaanan, B.
#3: Journal: J.Mol.Biol. / Year: 1984
Title: The Crystal Structure of Human Deoxyhemoglobin at 1.74 Angstroms Resolution
Authors: Fermi, G. / Perutz, M.F. / Shaanan, B. / Fourme, R.
#4: Journal: J.Biol.Chem. / Year: 1992
Title: A third quaternary structure of human hemoglobin A at 1.7-A resolution
Authors: Silva, M.M. / Rogers, P.H. / Arnone, A.
History
DepositionSep 11, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 11, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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.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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
P: Hemoglobin alpha chain
Q: Hemoglobin beta chain
R: Hemoglobin alpha chain
S: Hemoglobin beta chain
U: Hemoglobin alpha chain
V: Hemoglobin beta chain
W: Hemoglobin alpha chain
X: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)193,64124
Polymers186,24312
Non-polymers7,39812
Water00
1
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
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
P: Hemoglobin alpha chain
Q: Hemoglobin beta chain
R: Hemoglobin alpha chain
S: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
U: Hemoglobin alpha chain
V: Hemoglobin beta chain
W: Hemoglobin alpha chain
X: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5478
Polymers62,0814
Non-polymers2,4664
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.500, 57.900, 143.400
Angle α, β, γ (deg.)90.00, 101.20, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein
Hemoglobin alpha chain


Mass: 15150.353 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C34H32FeN4O4

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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: 2.53 Å3/Da / Density % sol: 51.4 %
Crystal growTemperature: 293 K / Method: liquid diffusion / pH: 6.7
Details: PEG 4000, Sodium potassium phosphate, pH 6.7, LIQUID DIFFUSION at 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.2→10 Å / Num. obs: 84268 / % possible obs: 92.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.108
Reflection shellResolution: 3.2→3.3 Å / Rmerge(I) obs: 0.379

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: HUMAN OXYHEMOGLOBIN

Resolution: 3.2→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 158735.8 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.245 1010 4.8 %RANDOM
Rwork0.204 ---
obs0.204 21043 69.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.9737 Å2 / ksol: 0.20873 e/Å3
Displacement parametersBiso mean: 85 Å2
Baniso -1Baniso -2Baniso -3
1--20.45 Å20 Å219.51 Å2
2--7.36 Å20 Å2
3---13.09 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.49 Å0.44 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.84 Å
Refinement stepCycle: LAST / Resolution: 3.2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13152 0 516 0 13668
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d18.8
X-RAY DIFFRACTIONc_improper_angle_d1.13
LS refinement shellResolution: 3.2→3.39 Å / Rfactor Rfree error: 0.043 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.376 78 5.1 %
Rwork0.364 1459 -
obs--30.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2PARAM19X.HEMETOPH19X.HEME
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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