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- PDB-6zmy: Crystal structure of hemoglobin from turkey (Meleagiris gallopova... -

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Basic information

Entry
Database: PDB / ID: 6zmy
TitleCrystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in monoclinic form at 1.66 Angstrom resolution
Components
  • Hemoglobin beta chain
  • Hemoglobin subunit alpha-A
KeywordsOXYGEN STORAGE/OXYGEN TRANSPORT / Hemoglobin / turkey / heme / meleagiris gallopova / monoclinic form / OXYGEN TRANSPORT / OXYGEN STORAGE / OXYGEN STORAGE-OXYGEN TRANSPORT complex
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 / Globin domain-containing protein / Hemoglobin subunit alpha-A / Hemoglobin beta chain
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.655 Å
AuthorsPandian, R. / Shobana, N. / Sundaresan, S.S. / Thangaraj, V. / Sayed, Y. / Ponnuswamy, M.N.
Funding support United Kingdom, Portugal, 2items
OrganizationGrant numberCountry
Science and Technology Funding CouncilST/R002754/1 United Kingdom
Foundation for Science and Technology (FCT)UIDB/04378/2020 Portugal
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
DepositionJul 4, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 15, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Derived calculations / Structure summary / Category: struct_conn / struct_keywords
Item: _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id ..._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_keywords.pdbx_keywords / _struct_keywords.text
Revision 1.2Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _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
Revision 1.3Jan 31, 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

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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 beta chain
C: Hemoglobin subunit alpha-A
D: Hemoglobin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7958
Polymers63,3294
Non-polymers2,4664
Water10,431579
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10830 Å2
ΔGint-100 kcal/mol
Surface area23590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.580, 80.520, 64.420
Angle α, β, γ (deg.)90.000, 96.300, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 15334.737 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P81023
#2: Protein Hemoglobin beta chain


Mass: 16329.866 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Meleagris gallopavo (turkey) / References: UniProt: P84479, UniProt: G1U9Q8*PLUS
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.44 % / Description: Block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 50% of PEG3350 in 50mM phosphate buffer at pH7.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jul 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 1.655→64.031 Å / Num. obs: 70052 / % possible obs: 98.9 % / Redundancy: 2.9 % / Biso Wilson estimate: 29.552 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.065 / Rrim(I) all: 0.08 / Net I/σ(I): 8.6
Reflection shellResolution: 1.655→1.684 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3465 / CC1/2: 0.484 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAW

1faw


Resolution: 1.655→64.031 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 27.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.25 3536 5.05 %
Rwork0.2 66514 -
obs0.2025 70050 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 82.05 Å2 / Biso mean: 26.0865 Å2 / Biso min: 6.55 Å2
Refinement stepCycle: final / Resolution: 1.655→64.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 172 579 5156
Biso mean--22.74 36.14 -
Num. residues----566
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.655-1.67770.38251690.3819265299
1.6777-1.70160.40171580.36372604100
1.7016-1.7270.38531490.36152649100
1.727-1.7540.36461530.34622669100
1.754-1.78280.36091200.32492698100
1.7828-1.81350.34671210.30122690100
1.8135-1.84650.31981560.29772665100
1.8465-1.8820.33961350.289268299
1.882-1.92040.30831390.2622267299
1.9204-1.96220.30441510.25042647100
1.9622-2.00790.26761420.23792692100
2.0079-2.05810.29131300.22162677100
2.0581-2.11370.24391480.21792678100
2.1137-2.17590.27081500.20282681100
2.1759-2.24620.23521470.1852664100
2.2462-2.32640.24851430.19272662100
2.3264-2.41960.24811410.181269499
2.4196-2.52970.25311360.1864266499
2.5297-2.66310.27131440.1817269299
2.6631-2.82990.28321400.193264899
2.8299-3.04840.24921330.1913267098
3.0484-3.35520.23471320.1763265098
3.3552-3.84070.21221380.1513258295
3.8407-4.83860.15461260.1394256594
4.8386-64.0310.20971350.1721266796

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