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- PDB-6kav: Carbonmonoxy human hemoglobin A in the R2 quaternary structure at... -

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Basic information

Entry
Database: PDB / ID: 6kav
TitleCarbonmonoxy human hemoglobin A in the R2 quaternary structure at 140 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 / 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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 24, 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 1.3Nov 22, 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 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

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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)64,65912
Polymers62,0814
Non-polymers2,5788
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11600 Å2
ΔGint-110 kcal/mol
Surface area23840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.146, 96.527, 100.224
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 15150.353 Da / Num. of mol.: 2 / 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.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.37 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5.8
Details: 18%w/v PEG6000, 100 mM sodium cacodylate-hydrochloride buffer, 10%v/v glycerol

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Data collection

DiffractionMean temperature: 140 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→19.77 Å / Num. obs: 64590 / % possible obs: 98.2 % / Redundancy: 6.5 % / Biso Wilson estimate: 20.11 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.084 / Rpim(I) all: 0.035 / Rrim(I) all: 0.091 / Net I/σ(I): 13.8 / Num. measured all: 421591 / Scaling rejects: 29
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
1.7-1.766.70.7524447366310.8190.310.8142.997.6
6.36-19.776.60.054810612270.9980.0220.05929.488.6

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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: 1BBB

1bbb


Resolution: 1.7→19.769 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 20.2
RfactorNum. reflection% reflection
Rfree0.2047 3267 5.06 %
Rwork0.175 --
obs0.1765 64532 97.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 98.83 Å2 / Biso mean: 24.7463 Å2 / Biso min: 8.99 Å2
Refinement stepCycle: final / Resolution: 1.7→19.769 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 180 326 4890
Biso mean--21.92 31.25 -
Num. residues----574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064712
X-RAY DIFFRACTIONf_angle_d0.9866450
X-RAY DIFFRACTIONf_chiral_restr0.038700
X-RAY DIFFRACTIONf_plane_restr0.005806
X-RAY DIFFRACTIONf_dihedral_angle_d12.9161600
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 23

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7-1.72540.26161540.21832577273197
1.7254-1.75230.29891270.212613274097
1.7523-1.7810.26211330.21182617275098
1.781-1.81170.23271330.20392639277298
1.8117-1.84460.24981560.20142565272197
1.8446-1.88010.24231300.2092667279798
1.8801-1.91840.24391420.20192633277597
1.9184-1.96010.20961440.18532621276598
1.9601-2.00570.25261280.18852669279798
2.0057-2.05580.2191330.18092651278498
2.0558-2.11130.23231590.18262636279598
2.1113-2.17330.21271440.17132652279699
2.1733-2.24340.19611380.16582667280599
2.2434-2.32350.19091510.1712651280299
2.3235-2.41630.19731450.17172670281599
2.4163-2.52610.21681450.17732679282499
2.5261-2.6590.20781430.1862691283498
2.659-2.82510.2211340.1862690282499
2.8251-3.04250.22541420.192717285999
3.0425-3.34740.19931310.19772737286899
3.3474-3.82870.18341620.16532716287898
3.8287-4.81230.17711350.14252762289799
4.8123-19.77030.16911580.14982745290394

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