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- PDB-3qjd: Human Hemoglobin A Mutant Alpha H58L Deoxy-Form -

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Basic information

Entry
Database: PDB / ID: 3qjd
TitleHuman Hemoglobin A Mutant Alpha H58L Deoxy-Form
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / ligand migration pathways / distal His / globin / oxygen / carbon monoxide / red blood cells
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 / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: Thesis
Title: Determination of Pathways for Oxygen Binding to Human HbA
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionJan 28, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_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
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,88112
Polymers62,0314
Non-polymers2,8508
Water16,556919
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-155 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.650, 82.070, 53.490
Angle α, β, γ (deg.)90.00, 99.51, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15125.364 Da / Num. of mol.: 2 / Mutation: H58L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBA1, HBA2 / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P69905
#2: Protein Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain / LVV-hemorphin-7


Mass: 15890.198 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBB / Plasmid: pHE2 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / 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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 919 / 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: 2.19 Å3/Da / Density % sol: 43.74 %
Crystal growTemperature: 293 K / Method: small tubes / pH: 6.5
Details: 2.4-2.6 M ammonium phosphate/sulfate, pH 6.5, SMALL TUBES, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 21, 2008
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→61.79 Å / Num. all: 94550 / Num. obs: 76521 / % possible obs: 80.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 2.8 % / Rsym value: 0.044 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsRsym value% possible all
1.45-1.51.51.90.16114.2
1.5-1.5642
1.56-1.6371.7
1.63-1.7293.9
1.72-1.8396
1.83-1.9796.7
1.97-2.1697.6
2.16-2.4898.3
2.48-3.1299.3
3.12-61.7998.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
d*TREKdata reduction
d*TREKdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DN2

2dn2


Resolution: 1.56→20.596 Å / SU ML: 0.19 / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 20.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1907 1851 2.61 %RANDOM
Rwork0.169 ---
all0.1696 75858 --
obs0.1696 70958 93.54 %-
Solvent computationShrinkage radii: 0.04 Å / VDW probe radii: 0.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 77.296 Å2 / ksol: 0.447 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.6703 Å20 Å2-0.4317 Å2
2--1.6311 Å20 Å2
3----0.9608 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20.596 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4380 0 192 919 5491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065039
X-RAY DIFFRACTIONf_angle_d1.1936965
X-RAY DIFFRACTIONf_dihedral_angle_d12.8631810
X-RAY DIFFRACTIONf_chiral_restr0.066752
X-RAY DIFFRACTIONf_plane_restr0.005881
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.56-1.60220.27741000.26623695X-RAY DIFFRACTION65
1.6022-1.64930.251240.23214695X-RAY DIFFRACTION83
1.6493-1.70250.2671440.21235351X-RAY DIFFRACTION94
1.7025-1.76340.2251440.19495373X-RAY DIFFRACTION95
1.7634-1.83390.22441460.19155416X-RAY DIFFRACTION96
1.8339-1.91730.2531440.18135466X-RAY DIFFRACTION96
1.9173-2.01830.18481460.1855493X-RAY DIFFRACTION97
2.0183-2.14470.22161490.17865527X-RAY DIFFRACTION97
2.1447-2.310.18181490.16335533X-RAY DIFFRACTION98
2.31-2.54210.18991500.15965603X-RAY DIFFRACTION98
2.5421-2.90910.19021500.16155623X-RAY DIFFRACTION99
2.9091-3.66180.17131530.15065670X-RAY DIFFRACTION99
3.6618-20.59810.15131520.15485662X-RAY DIFFRACTION98

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