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- PDB-4mqj: Structure of Wild-type Fetal Human Hemoglobin HbF -

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Basic information

Entry
Database: PDB / ID: 4mqj
TitleStructure of Wild-type Fetal Human Hemoglobin HbF
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / oxygen-transport / autooxidation
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process ...nitric oxide transport / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / cellular oxidant detoxification / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen / hydrogen peroxide catabolic process / oxygen carrier activity / 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 / Factors involved in megakaryocyte development and platelet production / blood microparticle / iron ion binding / heme binding / 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 family profile. / Globin-like / Globin / Globin / Globin-like superfamily ...Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit gamma-2 / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSoman, J. / Olson, J.S.
CitationJournal: To be Published
Title: Structure of Wild-type Fetal Human Hemoglobin HbF
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 1.1Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _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 / 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_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 gamma-2
G: Hemoglobin subunit alpha
H: Hemoglobin subunit gamma-2
C: Hemoglobin subunit alpha
D: Hemoglobin subunit gamma-2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,91521
Polymers124,8398
Non-polymers5,07613
Water22,0861226
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit gamma-2
G: Hemoglobin subunit alpha
H: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,94110
Polymers62,4194
Non-polymers2,5226
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11970 Å2
ΔGint-112 kcal/mol
Surface area23160 Å2
MethodPISA
2
C: Hemoglobin subunit alpha
D: Hemoglobin subunit gamma-2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit gamma-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,97311
Polymers62,4194
Non-polymers2,5547
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12240 Å2
ΔGint-115 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.651, 52.427, 106.153
Angle α, β, γ (deg.)90.00, 113.84, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Hemoglobin subunit ... , 2 types, 8 molecules AGCEBHDF

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


Mass: 15150.353 Da / Num. of mol.: 4
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 gamma-2 / / Gamma-2-globin / Hb F Ggamma / Hemoglobin gamma-2 chain / Hemoglobin gamma-G chain


Mass: 16059.308 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HBG2 / Production host: Escherichia coli (E. coli) / References: UniProt: P69892

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Non-polymers , 4 types, 1239 molecules

#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE / Carbon monoxide


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE / Oxygen


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1226 / 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: 2.15 Å3/Da / Density % sol: 42.9 %
Crystal growTemperature: 298 K / Method: liquid diffusion / pH: 7
Details: Protein crystallized from 1.9M Sodium/Potassium Phosphate, pH 7.0, Batch method, temperature 298K, LIQUID DIFFUSION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.07 Å
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: 1.8→100 Å / Num. obs: 99805 / % possible obs: 99.7 % / Redundancy: 7.4 % / Biso Wilson estimate: 17.57 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 13
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.837.20.439199.2
1.83-1.867.30.386199.3
1.86-1.97.30.33199.4
1.9-1.947.30.278199.6
1.94-1.987.30.234199.7
1.98-2.037.40.199199.9
2.03-2.087.40.17199.9
2.08-2.137.40.1481100
2.13-2.27.50.1341100
2.2-2.277.50.1231100
2.27-2.357.50.1141100
2.35-2.447.50.0991100
2.44-2.557.50.0931100
2.55-2.697.50.0821100
2.69-2.867.50.0781100
2.86-3.087.30.0751100
3.08-3.397.30.0671100
3.39-3.887.30.0541100
3.88-4.897.30.0481100
4.89-1006.90.046197.4

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→45.137 Å / Occupancy max: 1 / Occupancy min: 0.99 / SU ML: 0.2 / σ(F): 1.45 / Phase error: 21.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2151 2193 2 %
Rwork0.18 --
obs0.1805 97596 99.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 27.0233 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.137 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8789 0 354 1226 10369
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0159427
X-RAY DIFFRACTIONf_angle_d0.9312904
X-RAY DIFFRACTIONf_dihedral_angle_d13.4623216
X-RAY DIFFRACTIONf_chiral_restr0.0611404
X-RAY DIFFRACTIONf_plane_restr0.0051592
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7907-1.81250.30171190.23845843X-RAY DIFFRACTION85
1.8125-1.83550.30671440.23346700X-RAY DIFFRACTION99
1.8355-1.85960.29951390.22416843X-RAY DIFFRACTION99
1.8596-1.88510.20941310.21376811X-RAY DIFFRACTION99
1.8851-1.9120.25411390.21186726X-RAY DIFFRACTION99
1.912-1.94060.31381430.2116894X-RAY DIFFRACTION99
1.9406-1.97090.23281290.21326754X-RAY DIFFRACTION99
1.9709-2.00320.22221440.20266859X-RAY DIFFRACTION100
2.0032-2.03780.34871320.19756835X-RAY DIFFRACTION100
2.0378-2.07480.21321380.1926843X-RAY DIFFRACTION100
2.0748-2.11470.19951430.17826858X-RAY DIFFRACTION100
2.1147-2.15790.25511380.17236874X-RAY DIFFRACTION100
2.1579-2.20480.19491340.1716808X-RAY DIFFRACTION100
2.2048-2.25610.1941420.16876932X-RAY DIFFRACTION100
2.2561-2.31250.21621400.17276856X-RAY DIFFRACTION100
2.3125-2.3750.24841400.16896889X-RAY DIFFRACTION100
2.375-2.44490.22331420.17496794X-RAY DIFFRACTION100
2.4449-2.52380.21031460.18076917X-RAY DIFFRACTION100
2.5238-2.6140.22671420.17886866X-RAY DIFFRACTION100
2.614-2.71870.20551340.17736835X-RAY DIFFRACTION100
2.7187-2.84240.20731420.17926817X-RAY DIFFRACTION100
2.8424-2.99220.22961380.18436873X-RAY DIFFRACTION100
2.9922-3.17960.21771440.18316881X-RAY DIFFRACTION100
3.1796-3.4250.23561400.17426866X-RAY DIFFRACTION100
3.425-3.76960.15821460.15186862X-RAY DIFFRACTION100
3.7696-4.31470.15031380.14626870X-RAY DIFFRACTION100
4.3147-5.43460.16521400.16456854X-RAY DIFFRACTION100
5.4346-45.15170.27531380.21096545X-RAY DIFFRACTION95
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.9871-0.09660.01951.4341-0.48411.9615-0.00250.05660.09720.073-0.02330.1384-0.0798-0.08790.020.0662-0.00690.01430.1372-0.05260.1374-8.46469.76453.4291
21.9050.7824-0.11632.49990.49361.25250.07580.3866-0.2057-0.0234-0.0025-0.2620.13630.1033-0.09720.15930.0201-0.04780.3148-0.08320.13577.67943.883636.5166
31.7674-0.4728-0.70671.2331-0.2772.47570.0968-0.18540.15990.20020.02870.3355-0.14320.0017-0.08420.13-0.04140.06060.1803-0.05840.2123-40.310736.97333.9818
42.28780.5614-0.17272.54670.54421.79370.12040.0519-0.0661-0.00520.0228-0.21380.15330.2624-0.11060.12920.0184-0.04990.2281-0.0350.104-23.432631.854-12.6898
52.3043-0.217-1.26791.88350.15622.50080.0451-0.09120.2501-0.03570.08740.0828-0.46550.2029-0.06430.2045-0.0579-0.00350.1099-0.04660.1142-12.492940.050915.6672
62.0893-0.1519-1.26480.90710.0712.308-0.25540.1529-0.48760.02790.00810.12020.4814-0.14140.16060.2196-0.01290.08920.1263-0.03810.2594-18.095116.410513.4608
72.0904-0.0104-0.44792.1716-0.17972.1729-0.0826-0.01770.1650.05160.01680.1426-0.19220.00910.05390.1306-0.0268-0.02770.0725-0.02490.10819.016813.869964.559
82.0986-0.0234-0.4842.16130.35891.64420.01280.0279-0.3130.0696-0.0280.14780.1884-0.09860.0190.140.01330.00430.07820.010.173414.2136-9.890263.6613
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D
5X-RAY DIFFRACTION5chain E
6X-RAY DIFFRACTION6chain F
7X-RAY DIFFRACTION7chain G
8X-RAY DIFFRACTION8chain H

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