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

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Basic information

Entry
Database: PDB / ID: 6lcx
TitleCrosslinked alpha(Ni)-beta(Ni) human hemoglobin A in the T quaternary structure at 95 K: Light
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta
KeywordsOXYGEN TRANSPORT / Hemoglobin / Photolysis
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 / Heme signaling / Late endosomal microautophagy / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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
DepositionNov 20, 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 1.5Nov 13, 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)129,28518
Polymers124,1628
Non-polymers5,12310
Water25,2211400
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)64,6439
Polymers62,0814
Non-polymers2,5615
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11470 Å2
ΔGint-95 kcal/mol
Surface area23490 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)64,6439
Polymers62,0814
Non-polymers2,5615
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint-94 kcal/mol
Surface area23620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.815, 94.498, 100.510
Angle α, β, γ (deg.)90.000, 102.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 619.336 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C34H32N4NiO4
#4: Chemical ChemComp-2FU / BUT-2-ENEDIAL


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


Mass: 18.015 Da / Num. of mol.: 1400 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.6
Details: 1.0% (w/v) protein solution that contains 18% (w/v) PEG 3350, 0.15 M dipotassium sulfate, 50 mM citrate-ammonium buffer (pH 6.6)

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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 S 2M / Detector: PIXEL / Date: Oct 30, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→19.82 Å / Num. obs: 228030 / % possible obs: 98.2 % / Redundancy: 4.7 % / Biso Wilson estimate: 10.91 Å2 / CC1/2: 0.984 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.065 / Rrim(I) all: 0.147 / Net I/σ(I): 8.1 / Num. measured all: 1070625 / Scaling rejects: 14
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
1.4-1.454.80.36114497236220.9040.1780.4034.196.8
5.24-19.825.10.1212159742600.9770.0580.13512.293.3

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Processing

Software
NameVersionClassification
PHENIXdev_1839refinement
Aimless0.2.7data scaling
PDB_EXTRACT3.25data extraction
CrysalisProdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6KA9

6ka9


Resolution: 1.4→19.82 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.96
RfactorNum. reflection% reflection
Rfree0.2161 11433 5.01 %
Rwork0.1925 --
obs0.1936 228024 98.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.63 Å2 / Biso mean: 17.6164 Å2 / Biso min: 3.74 Å2
Refinement stepCycle: final / Resolution: 1.4→19.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8768 0 356 1400 10524
Biso mean--15.69 27.23 -
Num. residues----1148
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059414
X-RAY DIFFRACTIONf_angle_d0.92912908
X-RAY DIFFRACTIONf_chiral_restr0.0331400
X-RAY DIFFRACTIONf_plane_restr0.0051614
X-RAY DIFFRACTIONf_dihedral_angle_d12.4853204
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4-1.41590.28063890.244712197
1.4159-1.43260.27473620.2453711797
1.4326-1.450.26183700.2359710197
1.45-1.46840.27153680.2347709897
1.4684-1.48770.25743440.231712197
1.4877-1.50810.25373540.2273721497
1.5081-1.52960.26753960.225706097
1.5296-1.55240.25523650.2219716898
1.5524-1.57670.22273530.2159722498
1.5767-1.60250.22283590.2161712798
1.6025-1.63010.2373860.2117719098
1.6301-1.65980.25683820.219722898
1.6598-1.69170.25873490.2143717098
1.6917-1.72620.23183760.2132725198
1.7262-1.76370.24774070.2115720598
1.7637-1.80470.23024000.2064714498
1.8047-1.84980.2274080.2033724498
1.8498-1.89980.22983910.2053723099
1.8998-1.95560.22333940.2022723399
1.9556-2.01870.22624030.1942722999
2.0187-2.09070.21773950.1921730699
2.0907-2.17440.20173880.1885725999
2.1744-2.27320.23173760.1863728099
2.2732-2.39280.1954000.1832730799
2.3928-2.54250.22193690.1882729899
2.5425-2.73830.19944250.1897730999
2.7383-3.0130.20723940.1859733399
3.013-3.4470.20463720.18736799
3.447-4.33540.18173800.1582739999
4.3354-19.820.18173780.1695725897

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