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- PDB-6kai: Crosslinked alpha(Ni)-beta(Fe) human hemoglobin A in the T quater... -

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Basic information

Entry
Database: PDB / ID: 6kai
TitleCrosslinked alpha(Ni)-beta(Fe) human hemoglobin A in the T quaternary structure at 95 K: Light
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 / organic acid binding / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin 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 / carbon dioxide transport / Late endosomal microautophagy / Heme signaling / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / response to hydrogen peroxide / Cytoprotection by HMOX1 / platelet aggregation / oxygen binding / regulation of blood pressure / 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 / 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 ...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
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: 1.45 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 23, 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 / struct_conn
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
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 1.5Oct 9, 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)129,69433
Polymers124,1628
Non-polymers5,53225
Water23,6901315
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)64,83316
Polymers62,0814
Non-polymers2,75212
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-108 kcal/mol
Surface area23270 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)64,86117
Polymers62,0814
Non-polymers2,78013
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12920 Å2
ΔGint-111 kcal/mol
Surface area23380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.589, 94.415, 99.956
Angle α, β, γ (deg.)90.000, 101.970, 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, 1340 molecules

#3: Chemical
ChemComp-HNI / PROTOPORPHYRIN IX CONTAINING NI(II)


Mass: 619.336 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#4: Chemical
ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: CO
#5: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#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.: 1315 / 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: 2.4 Å3/Da / Density % sol: 48.78 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.6
Details: 20%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
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→19.88 Å / Num. obs: 202119 / % possible obs: 97.7 % / Redundancy: 4.5 % / Biso Wilson estimate: 12.71 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.043 / Rrim(I) all: 0.096 / Net I/σ(I): 10 / Num. measured all: 900680 / Scaling rejects: 431
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
1.45-1.53.80.27974590195620.8770.1540.323.490.1
5.43-19.885.10.071915537870.9930.0330.07818.193.8

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Processing

Software
NameVersionClassification
Aimless0.2.7data scaling
PHENIXdev_1839refinement
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1J40

1j40


Resolution: 1.45→19.88 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.5 / Phase error: 18.93
RfactorNum. reflection% reflection
Rfree0.2016 10185 5.04 %
Rwork0.1745 --
obs0.1759 202087 97.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 79.67 Å2 / Biso mean: 19.151 Å2 / Biso min: 5.23 Å2
Refinement stepCycle: final / Resolution: 1.45→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 386 1315 10469
Biso mean--18.48 29.3 -
Num. residues----1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059449
X-RAY DIFFRACTIONf_angle_d0.98912908
X-RAY DIFFRACTIONf_chiral_restr0.0341400
X-RAY DIFFRACTIONf_plane_restr0.0051614
X-RAY DIFFRACTIONf_dihedral_angle_d13.4543204
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 (%)
1.45-1.46650.23893210.22435722604387
1.4665-1.48370.26933150.2295845616090
1.4837-1.50180.24763380.22055995633392
1.5018-1.52080.2323390.20356099643894
1.5208-1.54080.22423240.20246160648494
1.5408-1.56190.23753270.19876240656796
1.5619-1.58420.21793240.19616328665296
1.5842-1.60790.22023420.1936314665697
1.6079-1.6330.24463090.19486434674398
1.633-1.65970.24433320.19146511684398
1.6597-1.68830.20983640.19026336670098
1.6883-1.7190.22643710.18896435680699
1.719-1.75210.24283470.1966472681999
1.7521-1.78780.2123520.18636457680999
1.7878-1.82670.20853330.18226459679299
1.8267-1.86910.20113400.18186477681799
1.8691-1.91580.18453540.18016493684799
1.9158-1.96760.22143530.18716533688699
1.9676-2.02540.21333220.17646515683799
2.0254-2.09070.20323700.17486511688199
2.0907-2.16540.19143590.172165196878100
2.1654-2.25190.2063470.170665206867100
2.2519-2.35430.2043320.169565386870100
2.3543-2.47820.1933690.171865326901100
2.4782-2.63310.20683460.171865736919100
2.6331-2.83590.19243260.169865696895100
2.8359-3.12030.2023660.173765596925100
3.1203-3.56960.19393230.168766386961100
3.5696-4.48870.17223140.146166156929100
4.4887-19.88510.16953260.16016503682997

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