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- PDB-3hrw: Crystal structure of hemoglobin from mouse (Mus musculus)at 2.8 -

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Basic information

Entry
Database: PDB / ID: 3hrw
TitleCrystal structure of hemoglobin from mouse (Mus musculus)at 2.8
Components
  • Hemoglobin subunit alpha
  • Hemoglobin subunit beta-1
KeywordsOXYGEN TRANSPORT / HEME / IRON / METAL-BINDING / Polymorphism / Transport / Phosphoprotein
Function / homology
Function and homology information


Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / hemoglobin beta binding / Scavenging of heme from plasma / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin binding ...Erythrocytes take up carbon dioxide and release oxygen / Erythrocytes take up oxygen and release carbon dioxide / hemoglobin beta binding / Scavenging of heme from plasma / regulation of eIF2 alpha phosphorylation by heme / response to stilbenoid / cellular oxidant detoxification / nitric oxide transport / hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / oxygen transport / hemopoiesis / erythrocyte development / hydrogen peroxide catabolic process / oxygen carrier activity / response to bacterium / carbon dioxide transport / oxygen binding / peroxidase activity / myelin sheath / cytosolic small ribosomal subunit / in utero embryonic development / blood microparticle / iron ion binding / heme binding / protein-containing complex binding / extracellular space / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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 / Hemoglobin subunit alpha / Hemoglobin subunit beta-1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSundaresan, S.S. / Ramesh, P. / Ponnuswamy, M.N.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2021
Title: Crystal structure of hemoglobin from mouse (Mus musculus) compared with those from other small animals and humans.
Authors: Sundaresan, S.S. / Ramesh, P. / Shobana, N. / Vinuchakkaravarthy, T. / Yasien, S. / Ponnuswamy, M.N.G.
History
DepositionJun 10, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 21, 2021Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 1, 2023Group: 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

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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-1
C: Hemoglobin subunit alpha
D: Hemoglobin subunit beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8888
Polymers61,4224
Non-polymers2,4664
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11100 Å2
ΔGint-104 kcal/mol
Surface area23330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.081, 65.940, 150.931
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 14978.991 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: RED BLOOD CELLS / References: UniProt: P01942
#2: Protein Hemoglobin subunit beta-1 / Hemoglobin beta-1 chain / Beta-1-globin / Hemoglobin beta-major chain


Mass: 15731.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Tissue: RED BLOOD CELLS / References: UniProt: P02088
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: May 8, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 2.8→19.94 Å / Num. obs: 12720 / % possible obs: 93 % / Redundancy: 2.61 % / Rsym value: 0.1135 / Net I/σ(I): 2.8
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 1.98 % / Mean I/σ(I) obs: 1 / Rsym value: 0.4242 / % possible all: 90

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASESphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1hab

1hab


Resolution: 2.8→19.94 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.843 / SU B: 18.606 / SU ML: 0.37 / Cross valid method: THROUGHOUT / ESU R Free: 0.549 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30561 616 4.9 %RANDOM
Rwork0.24259 ---
obs0.24547 11999 92.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 36.566 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→19.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4330 0 172 46 4548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214636
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5722.0546339
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5555570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.97423.75176
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.83715705
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3991512
X-RAY DIFFRACTIONr_chiral_restr0.0950.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023492
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2850.22776
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.23127
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.2244
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.160.23
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.260.264
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1070.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5291.52875
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.88624500
X-RAY DIFFRACTIONr_scbond_it1.01331971
X-RAY DIFFRACTIONr_scangle_it1.5174.51831
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.871 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 33 -
Rwork0.301 811 -
obs--88.94 %

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