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- PDB-4mqh: Structure of Aquomet Hemoglobin Evans alphaV62Mbetawt -

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Basic information

Entry
Database: PDB / ID: 4mqh
TitleStructure of Aquomet Hemoglobin Evans alphaV62Mbetawt
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / oxygen-transport / autooxidation
Function / homology
Function and homology information


nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin binding / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / renal absorption / organic acid binding / 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 / oxygen binding / regulation of blood pressure / platelet aggregation / Chaperone Mediated Autophagy / peroxidase activity / positive regulation of nitric oxide biosynthetic process / tertiary granule lumen / Factors involved in megakaryocyte development and platelet production / ficolin-1-rich granule lumen / blood microparticle / 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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: To be Published
Title: Structure of Aquomet Hemoglobin Evans alphaV62Mbetawt
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 1.1Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.location / _software.name / _software.type / _software.version
Revision 1.2Feb 28, 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_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

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Assembly

Deposited unit
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,9854
Polymers30,7522
Non-polymers1,2332
Water181
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)63,9708
Polymers61,5044
Non-polymers2,4664
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Unit cell
Length a, b, c (Å)52.926, 52.926, 194.139
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 14862.051 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: 15890.198 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1 / 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: 44.36 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 6.7
Details: Protein crystallized from 2.2M Sodium/Potassium Phosphate, pH 6.7, Batch method, temperature 298K, LIQUID DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5412 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5412 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 10243 / % possible obs: 98.9 % / Redundancy: 22.4 % / Rmerge(I) obs: 0.041 / Χ2: 1.134 / Net I/σ(I): 15
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.5421.10.5334600.929194.5
2.54-2.5920.90.5165000.943199.8
2.59-2.6420.80.424950.966198.6
2.64-2.6921.20.3294830.975198.2
2.69-2.7521.70.3035021.013199.8
2.75-2.8221.10.2394990.994198.2
2.82-2.8921.30.2125050.9961100
2.89-2.9621.60.1634981.015199.4
2.96-3.0522.40.1314910.981199.6
3.05-3.1521.70.1045140.956199.2
3.15-3.2622.70.0825081.0551100
3.26-3.3922.80.0715121.152199.8
3.39-3.5522.70.0635141.353199.4
3.55-3.7323.40.0485191.3061100
3.73-3.9723.40.0395081.254199.6
3.97-4.2723.80.0335221.195199.6
4.27-4.724.40.0315291.219199.6
4.7-5.3825.50.035411.21199.1
5.38-6.7825.70.0315461.395199.5
6.78-5019.80.0275971.52194.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
REFMACrefinement
PDB_EXTRACT3.11data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→35.771 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.36 / σ(F): 1.66 / Phase error: 26.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2499 1026 10.01 %
Rwork0.1921 --
obs0.1979 9159 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 207.48 Å2 / Biso mean: 70.9807 Å2 / Biso min: 22.01 Å2
Refinement stepCycle: LAST / Resolution: 2.5→35.771 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2169 0 86 1 2256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012329
X-RAY DIFFRACTIONf_angle_d1.1823195
Refinement TLS params.Method: refined / Origin x: -3.5597 Å / Origin y: 6.1393 Å / Origin z: 11.393 Å
111213212223313233
T0.3373 Å20.0408 Å20.0748 Å2-0.4206 Å2-0.0122 Å2--0.2456 Å2
L5.6991 °2-0.8544 °2-0.5378 °2-4.7098 °2-0.1649 °2--5.9556 °2
S-0.1352 Å °-0.3899 Å °-0.0685 Å °0.5931 Å °0.2592 Å °0.383 Å °0.0291 Å °-0.6621 Å °-0.0678 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 301
2X-RAY DIFFRACTION1allB1 - 201

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