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- PDB-6hk2: Crystal structure of ferric R-state human methemoglobin bound to ... -

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Basic information

Entry
Database: PDB / ID: 6hk2
TitleCrystal structure of ferric R-state human methemoglobin bound to maleimide-deferoxamine bifunctional chelator (DFO)
Components(Hemoglobin subunit ...) x 2
KeywordsOXYGEN TRANSPORT / DFO / COMPLEX / BETA CYS93
Function / homology
Function and homology information


cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma ...cellular oxidant detoxification / Heme assimilation / nitric oxide transport / hemoglobin alpha binding / hemoglobin binding / haptoglobin-hemoglobin complex / renal absorption / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / erythrocyte development / endocytic vesicle lumen / blood vessel diameter maintenance / hydrogen peroxide catabolic process / oxygen carrier activity / carbon dioxide transport / response to hydrogen peroxide / Erythrocytes take up oxygen and release carbon dioxide / Heme signaling / Erythrocytes take up carbon dioxide and release oxygen / Cytoprotection by HMOX1 / oxygen binding / Late endosomal microautophagy / platelet aggregation / 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 / inflammatory response / heme binding / Neutrophil degranulation / : / extracellular exosome / extracellular region / membrane / metal ion binding / 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
Chem-G7Z / PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCerutti, G. / Savino, C. / Montemiglio, L.C. / Boffi, A.
Funding support Italy, 2items
OrganizationGrant numberCountry
European Commission637295 Italy
European Commission312284 Italy
CitationJournal: Int J Mol Sci / Year: 2020
Title: Biodistribution PET/CT Study of Hemoglobin-DFO-89Zr Complex in Healthy and Lung Tumor-Bearing Mice.
Authors: Kiraga, L. / Cerutti, G. / Braniewska, A. / Strzemecki, D. / Sas, Z. / Boffi, A. / Savino, C. / Montemiglio, L.C. / Turnham, D. / Seaton, G. / Bonamore, A. / Clarkson, R. / Dabkowski, A.M. / ...Authors: Kiraga, L. / Cerutti, G. / Braniewska, A. / Strzemecki, D. / Sas, Z. / Boffi, A. / Savino, C. / Montemiglio, L.C. / Turnham, D. / Seaton, G. / Bonamore, A. / Clarkson, R. / Dabkowski, A.M. / Paisey, S.J. / Taciak, B. / Kucharzewska, P. / Rygiel, T.P. / Krol, M.
History
DepositionSep 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2019Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)65,62018
Polymers62,0814
Non-polymers3,53914
Water10,647591
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13170 Å2
ΔGint-196 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.807, 62.863, 153.594
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Hemoglobin subunit ... , 2 types, 4 molecules ACBD

#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

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Non-polymers , 5 types, 605 molecules

#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-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-G7Z / 3-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]-~{N}-methyl-propanamide


Mass: 184.192 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H12N2O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 591 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.28 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.8
Details: 2.4 M (NH4)2SO4, 0.23 M (NH4)2HPO4, 0.07 M (NH4)H2PO4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→76.8 Å / Num. obs: 139941 / % possible obs: 94.2 % / Redundancy: 4 % / Net I/σ(I): 25.9
Reflection shellResolution: 1.55→1.64 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.01 / Num. unique obs: 18776 / CC1/2: 0.87 / Rrim(I) all: 0.55 / % possible all: 78

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Processing

Software
NameVersionClassification
REFMAC5.8.0232refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P5Q

3p5q


Resolution: 1.55→48.69 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.956 / SU B: 4.367 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.091 / ESU R Free: 0.096 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21178 3620 4.9 %RANDOM
Rwork0.16663 ---
obs0.16882 70661 95.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 30.158 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.72 Å20 Å2
3----0.72 Å2
Refinement stepCycle: 1 / Resolution: 1.55→48.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 235 592 5211
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0135227
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174854
X-RAY DIFFRACTIONr_angle_refined_deg1.7441.7147225
X-RAY DIFFRACTIONr_angle_other_deg1.4731.62311293
X-RAY DIFFRACTIONr_dihedral_angle_1_deg16.015.263685
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3422.119236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.57915830
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2251518
X-RAY DIFFRACTIONr_chiral_restr0.0910.2617
X-RAY DIFFRACTIONr_gen_planes_refined0.010.026423
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021118
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8921.5142410
X-RAY DIFFRACTIONr_mcbond_other0.8911.5132409
X-RAY DIFFRACTIONr_mcangle_it1.4292.2653034
X-RAY DIFFRACTIONr_mcangle_other1.4292.2663035
X-RAY DIFFRACTIONr_scbond_it1.1481.7112817
X-RAY DIFFRACTIONr_scbond_other1.1041.6712788
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.712.4524105
X-RAY DIFFRACTIONr_long_range_B_refined6.55320.3076454
X-RAY DIFFRACTIONr_long_range_B_other6.43319.2176275
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 215 -
Rwork0.314 3945 -
obs--73.41 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.81720.7667-0.53550.9462-0.65772.4005-0.01080.00190.28160.1381-0.0998-0.1105-0.25470.19520.11070.0662-0.0131-0.03040.13160.08420.09122.4335-8.1183-7.8905
23.0201-0.27710.77061.4868-0.41092.4540.01550.3818-0.0464-0.2597-0.02440.00440.11410.23060.00890.0797-0.0253-0.00780.10250.01240.00775.8529-12.9941-24.8043
32.65161.0184-1.08952.6965-0.20742.890.0536-0.47530.07840.3823-0.02540.1869-0.1170.2525-0.02820.10450.01190.02330.1216-0.01970.07133.790515.6471-11.263
43.8044-0.94580.17091.2842-0.26731.99960.06310.1318-0.0448-0.1949-0.1261-0.14770.02120.27270.06310.1146-0.0360.0120.1120.03390.048919.898714.8326-29.3927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 202
2X-RAY DIFFRACTION2B1 - 202
3X-RAY DIFFRACTION3C1 - 202
4X-RAY DIFFRACTION4D1 - 202

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