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- PDB-4mqg: Structure of Carbonmonoxy Adult Hemoglobin Bristol-Alesha alphawt... -

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Basic information

Entry
Database: PDB / ID: 4mqg
TitleStructure of Carbonmonoxy Adult Hemoglobin Bristol-Alesha alphawtbetaV67M
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / oxygen-transport / autooxidation
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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 domain profile. / Globin-like / Globin / Globin ...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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.68 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: To be Published
Title: Structure of Carbonmonoxy Adult Hemoglobin Bristol-Alesha alphawtbetaV67M
Authors: Soman, J. / Olson, J.S.
History
DepositionSep 16, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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_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.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_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_ref_seq_dif.details / _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)32,3626
Polymers31,0732
Non-polymers1,2894
Water4,017223
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)64,72312
Polymers62,1454
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area11840 Å2
ΔGint-118 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.430, 53.430, 192.220
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-344-

HOH

21A-379-

HOH

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Components

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


Mass: 15150.353 Da / Num. of mol.: 1 / Mutation: V67M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15922.263 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Production host: Escherichia coli (E. coli) / References: UniProt: P68871
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 44.28 %
Crystal growTemperature: 298 K / pH: 7
Details: Protein crystallized from 1.9M Sodium/Potassium Phosphate, Batch method, pH 7.0, LIQUID DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.68→51.48 Å / Num. obs: 24312 / % possible obs: 74 % / Redundancy: 10.13 % / Biso Wilson estimate: 31.86 Å2 / Rmerge(I) obs: 0.127 / Net I/σ(I): 10.1
Reflection shellResolution: 1.68→1.74 Å / Redundancy: 3.52 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.3 / % possible all: 17.2

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Processing

Software
NameVersionClassificationNB
d*TREK9.9.9.4 W9RSSIdata reduction
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
d*TREKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: pdb entry 2DN3

2dn3


Resolution: 1.68→51.48 Å / Occupancy max: 1 / Occupancy min: 0.24 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 31.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.243 2000 8.23 %
Rwork0.199 --
obs0.203 24302 74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 1.68→51.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2193 0 90 223 2506
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0192350
X-RAY DIFFRACTIONf_angle_d1.0683225
X-RAY DIFFRACTIONf_dihedral_angle_d13.371799
X-RAY DIFFRACTIONf_chiral_restr0.065348
X-RAY DIFFRACTIONf_plane_restr0.006402
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6808-1.72280.4934280.4448313X-RAY DIFFRACTION15
1.7228-1.76940.4505470.3339520X-RAY DIFFRACTION25
1.7694-1.82140.3619640.319711X-RAY DIFFRACTION34
1.8214-1.88020.3034830.2755938X-RAY DIFFRACTION44
1.8802-1.94740.3141100.2541225X-RAY DIFFRACTION58
1.9474-2.02540.30011520.21111690X-RAY DIFFRACTION80
2.0254-2.11760.24611810.19862013X-RAY DIFFRACTION95
2.1176-2.22920.23941820.20362040X-RAY DIFFRACTION95
2.2292-2.36890.23731820.20422036X-RAY DIFFRACTION96
2.3689-2.55180.24931860.2092068X-RAY DIFFRACTION96
2.5518-2.80860.25751890.21282107X-RAY DIFFRACTION97
2.8086-3.21490.24061890.21592109X-RAY DIFFRACTION97
3.2149-4.05020.23421970.17312183X-RAY DIFFRACTION98
4.0502-51.50240.22682100.1892349X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 23.6868 Å / Origin y: 33.9731 Å / Origin z: 11.2472 Å
111213212223313233
T0.2247 Å2-0.0142 Å20.024 Å2-0.1985 Å2-0.0011 Å2--0.2084 Å2
L0.9588 °2-0.121 °20.1514 °2-0.32 °20.0792 °2--0.6735 °2
S-0.046 Å °0.0648 Å °-0.002 Å °0.0038 Å °0.0189 Å °0.0256 Å °-0.019 Å °-0.0532 Å °-0 Å °
Refinement TLS groupSelection details: all

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