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- PDB-6ka9: Crosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T qua... -

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Basic information

Entry
Database: PDB / ID: 6ka9
TitleCrosslinked alpha(Fe-CO)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K: Dark
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / Hemoglobin / Photolysis / Hybrid
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
BUT-2-ENEDIAL / CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / PROTOPORPHYRIN IX CONTAINING NI(II) / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsShibayama, N. / Park, S.Y. / Ohki, M. / Sato-Tomita, A.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP 16K07326 Japan
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2020
Title: Direct observation of ligand migration within human hemoglobin at work.
Authors: Shibayama, N. / Sato-Tomita, A. / Ohki, M. / Ichiyanagi, K. / Park, S.Y.
History
DepositionJun 21, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 4, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Mar 18, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 6, 2022Group: Database references / Derived calculations / Structure summary
Category: database_2 / struct ...database_2 / struct / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct.title / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.4Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / pdbx_validate_chiral
Revision 1.5Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,38622
Polymers124,1628
Non-polymers5,22314
Water29,9771664
1
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)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11800 Å2
ΔGint-101 kcal/mol
Surface area23330 Å2
MethodPISA
2
E: Hemoglobin subunit alpha
F: Hemoglobin subunit beta
G: Hemoglobin subunit alpha
H: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,69311
Polymers62,0814
Non-polymers2,6127
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11960 Å2
ΔGint-99 kcal/mol
Surface area23350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.639, 94.189, 100.317
Angle α, β, γ (deg.)90.000, 101.630, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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

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


Mass: 15150.353 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P69905
#2: Protein
Hemoglobin subunit beta / Beta-globin / Hemoglobin beta chain


Mass: 15890.198 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P68871

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Non-polymers , 5 types, 1678 molecules

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


Mass: 616.487 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#6: Chemical ChemComp-2FU / BUT-2-ENEDIAL


Mass: 84.073 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H4O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1664 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 48.94 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.6
Details: 18%w/v PEG 3350, 50 mM citrate-ammonium buffer, 150 mM dipotassium sulfate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 15, 2018
RadiationMonochromator: Si (111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.83 Å / Num. obs: 227212 / % possible obs: 98.4 % / Redundancy: 4.3 % / Biso Wilson estimate: 9.86 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.061 / Rpim(I) all: 0.031 / Rrim(I) all: 0.069 / Net I/σ(I): 13.8 / Num. measured all: 986182 / Scaling rejects: 39
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.4-1.453.90.32587392226690.8290.1750.3723.593.7
5.24-19.8350.042152043080.9980.020.04534.295

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J3Z

1j3z


Resolution: 1.4→19.829 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 17.75
RfactorNum. reflection% reflection
Rfree0.1911 11387 5.01 %
Rwork0.1659 --
obs0.1671 227200 98.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 73.47 Å2 / Biso mean: 15.516 Å2 / Biso min: 4.23 Å2
Refinement stepCycle: final / Resolution: 1.4→19.829 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 364 1664 10796
Biso mean--12.59 26.49 -
Num. residues----1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059442
X-RAY DIFFRACTIONf_angle_d1.00712908
X-RAY DIFFRACTIONf_chiral_restr0.0351400
X-RAY DIFFRACTIONf_plane_restr0.0061614
X-RAY DIFFRACTIONf_dihedral_angle_d13.4723204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4-1.41590.25853590.23626728708792
1.4159-1.43260.24723940.22296828722293
1.4326-1.450.23253500.21316846719695
1.45-1.46840.24794030.20827059746297
1.4684-1.48770.21413470.19917071741898
1.4877-1.50810.22813790.19327157753698
1.5081-1.52960.22253620.1897143750598
1.5296-1.55240.21883500.18127164751498
1.5524-1.57670.20684020.17757167756998
1.5767-1.60250.19023760.16977158753498
1.6025-1.63010.20973570.1747172752998
1.6301-1.65980.19634100.17167184759498
1.6598-1.69170.21773760.17537151752799
1.6917-1.72620.21113600.17277269762999
1.7262-1.76370.2054190.16857197761699
1.7637-1.80470.19434280.17287192762099
1.8047-1.84980.20543790.16957240761999
1.8498-1.89980.19113630.1677286764999
1.8998-1.95560.18553660.166273047670100
1.9556-2.01870.19173650.167572877652100
2.0187-2.09080.18973860.161172887674100
2.0908-2.17440.17923990.156372617660100
2.1744-2.27320.17043640.154973187682100
2.2732-2.39290.19613890.157673267715100
2.3929-2.54250.19373880.159773177705100
2.5425-2.73830.19083400.163573317671100
2.7383-3.0130.18894020.163773437745100
3.013-3.44710.18883670.164473627729100
3.4471-4.33540.16014070.139973737780100
4.3354-19.83070.16294000.15437291769198

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