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- PDB-6kap: Carbonmonoxy human hemoglobin C in the R quaternary structure at ... -

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Basic information

Entry
Database: PDB / ID: 6kap
TitleCarbonmonoxy human hemoglobin C in the R 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 / 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: 1.45 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 1.3Nov 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3306
Polymers31,0412
Non-polymers1,2894
Water1,874104
1
A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules

A: Hemoglobin subunit alpha
B: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,65912
Polymers62,0814
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_645y+1,x-1,-z1
Buried area11810 Å2
ΔGint-116 kcal/mol
Surface area23540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.526, 53.526, 192.768
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 15150.353 Da / Num. of mol.: 1 / 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: 15890.265 Da / Num. of mol.: 1 / 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.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.22 Å3/Da / Density % sol: 44.7 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.2
Details: 0.528 M sodium dihydrogen phosphate, 1.122 M dipotassium hydrogen phosphate, 10%v/v glycerol

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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: Nov 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.45→18.92 Å / Num. obs: 50776 / % possible obs: 99.8 % / Redundancy: 11.1 % / Biso Wilson estimate: 19.16 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.021 / Rrim(I) all: 0.07 / Net I/σ(I): 18 / Num. measured all: 562321 / Scaling rejects: 32
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
1.45-1.511.20.7885805551630.8820.2370.8232.999.3
5.43-18.9210.50.0531127810720.9980.0170.0564096.1

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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: 3S66

3s66


Resolution: 1.45→18.92 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.74
RfactorNum. reflection% reflection
Rfree0.2108 2576 5.08 %
Rwork0.1929 --
obs0.1938 50716 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 114.87 Å2 / Biso mean: 29.8494 Å2 / Biso min: 12.63 Å2
Refinement stepCycle: final / Resolution: 1.45→18.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2192 0 91 104 2387
Biso mean--25.52 32.48 -
Num. residues----287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062355
X-RAY DIFFRACTIONf_angle_d1.0143222
X-RAY DIFFRACTIONf_chiral_restr0.036350
X-RAY DIFFRACTIONf_plane_restr0.006401
X-RAY DIFFRACTIONf_dihedral_angle_d11.842800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4501-1.47790.20311450.23112566271199
1.4779-1.50810.23291340.22462607274199
1.5081-1.54090.26951390.21492636277599
1.5409-1.57670.22991610.212126382799100
1.5767-1.61610.2311450.201325922737100
1.6161-1.65980.23271520.202626092761100
1.6598-1.70860.23261330.201926352768100
1.7086-1.76370.21341330.196926632796100
1.7637-1.82670.20311290.194126352764100
1.8267-1.89980.2071320.193327052837100
1.8998-1.98610.21831340.194126702804100
1.9861-2.09070.21531330.191726662799100
2.0907-2.22150.22861560.189526872843100
2.2215-2.39280.21631660.195626562822100
2.3928-2.6330.21711390.20127172856100
2.633-3.01270.24131570.2127352892100
3.0127-3.79060.21171460.192127902936100
3.7906-18.9260.16981420.17342933307599
Refinement TLS params.Method: refined / Origin x: 23.6815 Å / Origin y: -19.766 Å / Origin z: 11.3054 Å
111213212223313233
T0.1756 Å20.0144 Å20.056 Å2-0.1388 Å20.0007 Å2--0.147 Å2
L1.1036 °2-0.1309 °2-0.0843 °2-0.6752 °20.3004 °2--0.9988 °2
S-0.0408 Å °0.094 Å °-0.033 Å °0.1138 Å °0.0193 Å °0.0601 Å °-0.0782 Å °-0.1442 Å °-0.0646 Å °
Refinement TLS groupSelection details: all

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