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

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Basic information

Entry
Database: PDB / ID: 6zmx
TitleCrystal structure of hemoglobin from turkey (Meleagiris gallopova) crystallized in orthorhombic form at 1.4 Angstrom resolution
Components
  • Hemoglobin beta chain
  • Hemoglobin subunit alpha-A
KeywordsOXYGEN STORAGE/OXYGEN TRANSPORT / Hemoglobin / turkey / heme / meleagiris gallopova / orthorhombic form / OXYGEN TRANSPORT / OXYGEN STORAGE / OXYGEN STORAGE-OXYGEN TRANSPORT complex
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / iron ion binding / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, pi / Hemoglobin, alpha-type / Hemoglobin, beta-type / Globin/Protoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin subunit alpha-A / Hemoglobin beta chain
Similarity search - Component
Biological speciesMeleagris gallopavo (turkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.389 Å
AuthorsPandian, R. / Shobana, N. / Sundaresan, S.S. / 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 22, 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)65,8189
Polymers63,3294
Non-polymers2,4895
Water8,773487
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10740 Å2
ΔGint-101 kcal/mol
Surface area23730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.760, 82.140, 90.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 1:40 or resseq 42:67 or resseq...
21(chain C and (resseq 1:40 or resseq 42:67 or resseq...
12(chain D and (resseq 1:13 or (resid 14 and (name...
22(chain B and (resseq 1:13 or (resid 14 and (name...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 40
121(chain A and (resseq 1:40 or resseq 42:67 or resseq...A42 - 67
131(chain A and (resseq 1:40 or resseq 42:67 or resseq...A69 - 81
141(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
151(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
161(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
171(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
181(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
191(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
1101(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
1111(chain A and (resseq 1:40 or resseq 42:67 or resseq...A1 - 150
211(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 40
221(chain C and (resseq 1:40 or resseq 42:67 or resseq...C42 - 67
231(chain C and (resseq 1:40 or resseq 42:67 or resseq...C0
241(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
251(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
261(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
271(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
281(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
291(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
2101(chain C and (resseq 1:40 or resseq 42:67 or resseq...C1 - 150
112(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 13
122(chain D and (resseq 1:13 or (resid 14 and (name...D14
132(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
142(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
152(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
162(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
172(chain D and (resseq 1:13 or (resid 14 and (name...D1 - 150
212(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 13
222(chain B and (resseq 1:13 or (resid 14 and (name...B14
232(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
242(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
252(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
262(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150
272(chain B and (resseq 1:13 or (resid 14 and (name...B1 - 150

NCS ensembles :
ID
1
2

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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
#3: Chemical
ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 487 / 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: 2.25 Å3/Da / Density % sol: 45.46 % / Description: Block
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 / Details: 40% of PEG 3350 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: 1.389→60.835 Å / Num. obs: 118908 / % possible obs: 99 % / Redundancy: 4.4 % / Biso Wilson estimate: 26.287 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.084 / Rrim(I) all: 0.096 / Net I/σ(I): 7.4
Reflection shellResolution: 1.389→1.413 Å / Redundancy: 4.4 % / Num. unique obs: 5867 / CC1/2: 0.514 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FAW

1faw


Resolution: 1.389→60.835 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2233 5918 4.98 %
Rwork0.1969 112980 -
obs0.1983 118898 98.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.53 Å2 / Biso mean: 28.6232 Å2 / Biso min: 9.26 Å2
Refinement stepCycle: final / Resolution: 1.389→60.835 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4402 0 173 489 5064
Biso mean--24.28 41.15 -
Num. residues----568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074920
X-RAY DIFFRACTIONf_angle_d0.9056763
X-RAY DIFFRACTIONf_chiral_restr0.068740
X-RAY DIFFRACTIONf_plane_restr0.006842
X-RAY DIFFRACTIONf_dihedral_angle_d20.4021707
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1194X-RAY DIFFRACTION6.954TORSIONAL
12C1194X-RAY DIFFRACTION6.954TORSIONAL
21D1272X-RAY DIFFRACTION6.954TORSIONAL
22B1272X-RAY DIFFRACTION6.954TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3891-1.40490.42221890.3937370298
1.4049-1.42140.39671870.3822374299
1.4214-1.43880.38411730.3705373499
1.4388-1.4570.34811870.3528375299
1.457-1.47620.33751750.3518372599
1.4762-1.49640.3661920.3386374399
1.4964-1.51780.32131840.3312372599
1.5178-1.54040.30671820.3046375599
1.5404-1.56450.30692010.2805366197
1.5645-1.59020.29782140.2743375899
1.5902-1.61760.28812040.2501371399
1.6176-1.6470.25362290.23223735100
1.647-1.67870.24392190.22773751100
1.6787-1.71290.25291850.21183778100
1.7129-1.75020.23891830.21733783100
1.7502-1.79090.2431990.21263765100
1.7909-1.83570.23082170.20983751100
1.8357-1.88530.22441970.20823794100
1.8853-1.94080.22941830.19963803100
1.9408-2.00350.23191650.20193820100
2.0035-2.07510.23722080.20273777100
2.0751-2.15820.23081920.1904374798
2.1582-2.25640.22541960.187374098
2.2564-2.37530.20961940.1874377499
2.3753-2.52420.22211870.1844380599
2.5242-2.71910.22051820.1839382499
2.7191-2.99270.22552160.1867377798
2.9927-3.42570.22082330.177375698
3.4257-4.31590.1792230.1534378697
4.3159-60.8350.17782220.1634400498

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