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- PDB-3at6: Side-necked turtle (Pleurodira, Chelonia, REPTILIA) hemoglobin: c... -

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Basic information

Entry
Database: PDB / ID: 3at6
TitleSide-necked turtle (Pleurodira, Chelonia, REPTILIA) hemoglobin: cDNA-derived primary structures and X-ray crystal structures of Hb A
Components
  • AlphaA-globin
  • Beta-globin
KeywordsOXYGEN TRANSPORT / HEMOGLOBIN A / Podocnemis unifilis / Pleurodira / Chelonia / REPTILIA / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / blood microparticle ...hemoglobin alpha binding / haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / oxygen binding / peroxidase activity / 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 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 / AlphaA-globin / Beta-globin
Similarity search - Component
Biological speciesPodocnemis unifilis (yellow-spotted Amazon River turtle)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsHasegawa, T. / Shishikura, F. / Kuwada, T.
CitationJournal: Iubmb Life / Year: 2011
Title: Side-necked turtle (Pleurodira, Chelonia, reptilia) hemoglobin: cDNA-derived primary structures and X-ray crystal structures of Hb A.
Authors: Hasegawa, T. / Shishikura, F. / Kuwada, T.
History
DepositionDec 26, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: AlphaA-globin
B: Beta-globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2044
Polymers31,9722
Non-polymers1,2332
Water2,162120
1
A: AlphaA-globin
B: Beta-globin
hetero molecules

A: AlphaA-globin
B: Beta-globin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,4098
Polymers63,9434
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_765-x+2,-x+y+1,-z+2/31
Buried area10630 Å2
ΔGint-95 kcal/mol
Surface area25900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.994, 65.994, 284.823
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein AlphaA-globin


Mass: 15618.856 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Podocnemis unifilis (yellow-spotted Amazon River turtle)
Tissue fraction: red blood cells / References: UniProt: E5RWQ0
#2: Protein Beta-globin


Mass: 16352.661 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Podocnemis unifilis (yellow-spotted Amazon River turtle)
Tissue fraction: red blood cells / References: UniProt: E5RWQ1
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.8 Å3/Da / Density % sol: 56.07 %

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Dec 24, 2008 / Details: CMF
RadiationMonochromator: Rigaku VariMax-HR CMF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→33.15 Å / Num. all: 14223 / Num. obs: 14223 / % possible obs: 87.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.28 % / Biso Wilson estimate: 32.1 Å2 / Rmerge(I) obs: 0.136 / Net I/σ(I): 5.7
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.53 % / Rmerge(I) obs: 0.354 / Mean I/σ(I) obs: 3.5 / Num. unique all: 1582 / % possible all: 99.7

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Processing

Software
NameVersionClassification
CrystalCleardata collection
EPMRphasing
CNX2002refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3AT5

3at5


Resolution: 2.35→33.15 Å / Rfactor Rfree error: 0.011 / Data cutoff high absF: 412255.15 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.295 710 5 %RANDOM
Rwork0.24 ---
all-14120 --
obs-14120 86.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 71.45 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.02 Å28.05 Å20 Å2
2--3.02 Å20 Å2
3----6.03 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.35→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2265 0 86 120 2471
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d17.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it4.21.5
X-RAY DIFFRACTIONc_mcangle_it6.192
X-RAY DIFFRACTIONc_scbond_it5.82
X-RAY DIFFRACTIONc_scangle_it7.582.5
LS refinement shellResolution: 2.35→2.5 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.313 116 4.5 %
Rwork0.245 2463 -
obs--98.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4hem.paramhem.top

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