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- PDB-3fs4: Crystal structure determination of Ostrich hemoglobin at 2.2 Angs... -

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Basic information

Entry
Database: PDB / ID: 3fs4
TitleCrystal structure determination of Ostrich hemoglobin at 2.2 Angstrom resolution
Components
  • Hemoglobin subunit alpha-A
  • Hemoglobin subunit beta
KeywordsOXYGEN STORAGE / OXYGEN TRANSPORT / Hemoglobin / Avian Species / Ostrich / quaternary structure / Heme / Iron / Metal-binding / Polymorphism / Transport
Function / homology
Function and homology information


haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding ...haptoglobin binding / organic acid binding / haptoglobin-hemoglobin complex / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / iron ion binding / heme binding / metal ion binding
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
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin subunit alpha-A / Hemoglobin subunit beta
Similarity search - Component
Biological speciesStruthio camelus (African ostrich)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsSundaresan, S.S. / Ramesh, P. / Sivakumar, K. / Ponnuswamy, M.N.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2021
Title: Structural studies of hemoglobin from two flightless birds, ostrich and turkey: insights into their differing oxygen-binding properties.
Authors: Ramesh, P. / Sundaresan, S.S. / Shobana, N. / Vinuchakkaravarthy, T. / Sivakumar, K. / Yasien, S. / Ponnuswamy, M.N.G.
History
DepositionJan 9, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 31, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 12, 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _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 1.3May 19, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Nov 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-A
B: Hemoglobin subunit beta
C: Hemoglobin subunit alpha-A
D: Hemoglobin subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,17112
Polymers63,5774
Non-polymers2,5948
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11930 Å2
ΔGint-103 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.794, 81.573, 101.450
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-A / Hemoglobin alpha-A chain / Alpha-A-globin


Mass: 15470.804 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Struthio camelus (African ostrich) / References: UniProt: P01981
#2: Protein Hemoglobin subunit beta / Hemoglobin beta chain / Beta-globin


Mass: 16317.874 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Struthio camelus (African ostrich) / References: UniProt: P02123
#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.: 4 / Source method: obtained synthetically / Formula: O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.63 Å3/Da / Density % sol: 53.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 20% PEG 3350, 50mM Na Phosphate buffer, pH 7.20, 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: 1.54159 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 10, 2008
RadiationMonochromator: Nil / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54159 Å / Relative weight: 1
ReflectionResolution: 2.22→29.6 Å / Num. all: 33356 / Num. obs: 33356 / Redundancy: 3.91 % / Rsym value: 0.063 / Net I/σ(I): 6.5
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 3.67 % / Mean I/σ(I) obs: 1.7 / Rsym value: 0.231

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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 1FAW

1faw


Resolution: 2.22→27.62 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.924 / SU B: 5.774 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.316 / ESU R Free: 0.23 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25602 1668 5 %RANDOM
Rwork0.21562 ---
obs0.21765 31682 99.2 %-
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: 44.544 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.22→27.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4485 0 180 270 4935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0224797
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5752.0556558
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4235570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.37823.918194
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.65215776
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9451518
X-RAY DIFFRACTIONr_chiral_restr0.1130.2715
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023596
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2240.22596
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.30.23306
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.2285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.20.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1420.227
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.7370.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0571.52932
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.45624595
X-RAY DIFFRACTIONr_scbond_it2.6832127
X-RAY DIFFRACTIONr_scangle_it3.6274.51955
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.224→2.281 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 116 -
Rwork0.264 2146 -
obs--92.21 %

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