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- PDB-3nmm: Human Hemoglobin A mutant alpha H58W deoxy-form -

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Basic information

Entry
Database: PDB / ID: 3nmm
TitleHuman Hemoglobin A mutant alpha H58W deoxy-form
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Hemoglobin / ligand migration pathways
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: 1.6 Å
AuthorsBirukou, I. / Soman, J. / Olson, J.S.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Blocking the gate to ligand entry in human hemoglobin.
Authors: Birukou, I. / Soman, J. / Olson, J.S.
History
DepositionJun 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 14, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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)64,83510
Polymers62,1774
Non-polymers2,6586
Water12,502694
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11660 Å2
ΔGint-126 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.550, 81.830, 53.450
Angle α, β, γ (deg.)90.000, 99.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15198.417 Da / Num. of mol.: 2 / Mutation: H59W
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 / Hemoglobin beta chain / Beta-globin / 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.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 694 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: batch method / pH: 6.5
Details: 20 ul Protein Solution (60mg/ml protein in 0.01 M ammonium phosphate pH 7.0) mixed with 100 ul mother liquor (0.5 ml 2M monobasic ammonium phosphate + 1.5 ml 2 M dibasic ammonium phosphate + ...Details: 20 ul Protein Solution (60mg/ml protein in 0.01 M ammonium phosphate pH 7.0) mixed with 100 ul mother liquor (0.5 ml 2M monobasic ammonium phosphate + 1.5 ml 2 M dibasic ammonium phosphate + 8 ml 4 M ammonium sulfate) for final concentrations of 2.4-2.6 M Ammonium phosphate/sulfate, Batch Method, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 20, 2009
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→52.67 Å / Num. obs: 62570 / % possible obs: 89.5 % / Observed criterion σ(I): 5 / Redundancy: 2.83 % / Rmerge(I) obs: 0.038 / Χ2: 1.01 / Net I/σ(I): 15.9 / Scaling rejects: 1338
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allΧ2% possible all
1.6-1.662.640.2314.21334350380.8972.3
1.66-1.722.860.2054.91713959890.9486.1
1.72-1.82.840.1675.81707660070.986.4
1.8-1.92.80.1377.11691860240.9286.1
1.9-2.022.740.1138.61686561520.988.4
2.02-2.172.70.08211.81715363430.991
2.17-2.392.730.06215.11800165710.8994.2
2.39-2.742.940.05318.61988167210.9396
2.74-3.453.010.04525.92080868281.0397.1
3.45-52.672.950.03245.92112168971.5997.1

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Processing

Software
NameVersionClassificationNB
d*TREKdata scaling
PHENIX1.6.1_357refinement
PDB_EXTRACT3.1data extraction
CrystalCleardata collection
d*TREKdata reduction
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2DN2

2dn2


Resolution: 1.6→28.817 Å / Occupancy max: 1 / Occupancy min: 0.21 / SU ML: 0.28 / Cross valid method: THROUGHOUT / σ(F): 1 / Phase error: 18.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 1993 3.22 %random
Rwork0.1733 ---
obs0.1741 61818 88.01 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.765 Å2 / ksol: 0.444 e/Å3
Displacement parametersBiso max: 90.56 Å2 / Biso mean: 22.6389 Å2 / Biso min: 9.31 Å2
Baniso -1Baniso -2Baniso -3
1--0.5846 Å20 Å2-0.7569 Å2
2--1.583 Å20 Å2
3----0.9984 Å2
Refinement stepCycle: LAST / Resolution: 1.6→28.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4392 0 182 694 5268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134815
X-RAY DIFFRACTIONf_angle_d1.5716632
X-RAY DIFFRACTIONf_chiral_restr0.081718
X-RAY DIFFRACTIONf_plane_restr0.009829
X-RAY DIFFRACTIONf_dihedral_angle_d13.6921665
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.63780.22041010.16293045314663
1.6378-1.6820.24041370.16434090422785
1.682-1.73150.19291400.15864155429586
1.7315-1.78740.2291370.15374145428285
1.7874-1.85130.20091390.14644149428886
1.8513-1.92540.16981380.14654190432887
1.9254-2.0130.20341430.14444279442288
2.013-2.11910.17411460.1374352449890
2.1191-2.25180.16641500.12854488463893
2.2518-2.42560.16111520.12374601475395
2.4256-2.66950.15971560.13384650480696
2.6695-3.05540.16021560.14114690484696
3.0554-3.84810.16571530.14174586473994
3.8481-28.82210.1941450.18094405455089

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