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- PDB-2w6v: Structure of Human deoxy Hemoglobin A in complex with Xenon -

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Basic information

Entry
Database: PDB / ID: 2w6v
TitleStructure of Human deoxy Hemoglobin A in complex with Xenon
Components(HEMOGLOBIN SUBUNIT ...) x 2
KeywordsOXYGEN TRANSPORT / PACKING DEFECTS / HYDROPHOBIC CAVITIES
Function / homology
Function and homology information


nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / hemoglobin complex / oxygen transport / Scavenging of heme from plasma / endocytic vesicle lumen ...nitric oxide transport / hemoglobin alpha binding / cellular oxidant detoxification / hemoglobin binding / renal absorption / haptoglobin-hemoglobin complex / 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 / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / Late endosomal microautophagy / Cytoprotection by HMOX1 / response to hydrogen peroxide / 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 / 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 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
PROTOPORPHYRIN IX CONTAINING FE / PHOSPHATE ION / XENON / Hemoglobin subunit beta / Hemoglobin subunit alpha
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsMiele, A.E. / Draghi, F. / Sciara, G. / Johnson, K.A. / Renzi, F. / Vallone, B. / Brunori, M. / Savino, C.
CitationJournal: Biopolymers / Year: 2009
Title: Pattern of Cavities in Globins: The Case of Human Hemoglobin.
Authors: Savino, C. / Miele, A.E. / Draghi, F. / Johnson, K.A. / Sciara, G. / Brunori, M. / Vallone, B.
History
DepositionDec 19, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2011Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Version format compliance
Revision 1.2Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_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)66,90129
Polymers62,0814
Non-polymers4,82025
Water10,377576
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-201.9 kcal/mol
Surface area23080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.645, 82.328, 53.552
Angle α, β, γ (deg.)90.00, 99.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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HEMOGLOBIN SUBUNIT ... , 2 types, 4 molecules ACBD

#1: Protein HEMOGLOBIN SUBUNIT ALPHA / HUMAN HEMOGLOBIN A / HEMOGLOBIN ALPHA CHAIN / ALPHA-GLOBIN


Mass: 15150.353 Da / Num. of mol.: 2 / Fragment: CHAIN ALPHA, RESIDUES 2-142 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: RED BLOOD CELL / Tissue: BLOOD / References: UniProt: P69905
#2: Protein HEMOGLOBIN SUBUNIT BETA / HUMAN HEMOGLOBIN B / HEMOGLOBIN BETA CHAIN / BETA-GLOBIN


Mass: 15890.198 Da / Num. of mol.: 2 / Fragment: CHAIN BETA, RESIDUES 2-147 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: RED BLOOD CELL / Tissue: BLOOD / References: UniProt: P68871

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Non-polymers , 6 types, 601 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-XE / XENON


Mass: 131.293 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Xe
#7: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 576 / Source method: isolated from a natural source / Formula: H2O

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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: 42.19 % / Description: NONE
Crystal growpH: 6.5
Details: 3.2M (NH4)2SO4, 0.1M (NH4)H2PO4, 0.3M (NH4)2HPO4, PH 6.5, 0.2% DITHIONITE.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9998
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9998 Å / Relative weight: 1
ReflectionResolution: 1.8→61 Å / Num. obs: 49841 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 4.3 % / Biso Wilson estimate: 21.85 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.5
Reflection shellResolution: 1.79→1.94 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 2.5 / % possible all: 97.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HHB

4hhb


Resolution: 1.8→22.9 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.941 / SU B: 3.007 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.139 / ESU R Free: 0.135 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED REGIONS WERE MODELLED STEREOCHEMICALLY AND THEIR OCCUPANCY PUT TO 0.0
RfactorNum. reflection% reflectionSelection details
Rfree0.216 2502 5 %RANDOM
Rwork0.162 ---
obs0.165 47136 99.7 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.57 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.01 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.8→22.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4384 0 240 576 5200
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0225105
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6242.0587070
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.9545660
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.89824.098205
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69615792
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5021514
X-RAY DIFFRACTIONr_chiral_restr0.10.2761
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023918
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2220.22855
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2950.23427
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2477
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.283
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2110.235
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7391.53035
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.19324920
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.12232194
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.1324.52112
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.84 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.476 171
Rwork0.346 3366

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