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- PDB-2z6n: Crystal Structure of Carbonmonoxy Hemoglobin D from the Aldabra G... -

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Basic information

Entry
Database: PDB / ID: 2z6n
TitleCrystal Structure of Carbonmonoxy Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea
Components
  • Hemoglobin A/D subunit beta
  • Hemoglobin D subunit alpha
KeywordsTRANSPORT PROTEIN / HEMOGLOBIN D / REPTILIA / THE ALDABRA GIANT TORTOISE / Geochelone gigantea / Heme / Iron / Metal-binding / Oxygen transport / Transport
Function / homology
Function and homology information


haptoglobin binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle / heme binding / metal ion binding
Similarity search - Function
Hemoglobin, alpha-type / Hemoglobin, beta-type / : / Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily ...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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Hemoglobin A/D subunit beta / Hemoglobin D subunit alpha
Similarity search - Component
Biological speciesDipsochelys dussumieri (Aldabra giant tortoise)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsKuwada, T. / Hasegawa, T. / Sato, I. / Ishikawa, K. / Shishikura, F.
CitationJournal: To be Published
Title: Crystal Structure of the Ligated Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea
Authors: Kuwada, T. / Hasegawa, T. / Sato, I. / Ishikawa, K. / Shishikura, F.
History
DepositionAug 4, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.name
Revision 1.3Nov 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

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Assembly

Deposited unit
A: Hemoglobin D subunit alpha
B: Hemoglobin A/D subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6746
Polymers32,3852
Non-polymers1,2894
Water6,936385
1
A: Hemoglobin D subunit alpha
B: Hemoglobin A/D subunit beta
hetero molecules

A: Hemoglobin D subunit alpha
B: Hemoglobin A/D subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,34812
Polymers64,7704
Non-polymers2,5788
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.355, 62.104, 53.987
Angle α, β, γ (deg.)90.00, 110.22, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a hemoglobin tetramer generated from the alpha-beta dimer in the asymmetric unit by the operation: -x, y, -z.

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Components

#1: Protein Hemoglobin D subunit alpha / Hemoglobin D alpha chain


Mass: 16190.386 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dipsochelys dussumieri (Aldabra giant tortoise)
Tissue: red blood cell / References: UniProt: P83134
#2: Protein Hemoglobin A/D subunit beta / Hemoglobin A/D beta chain


Mass: 16194.624 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Dipsochelys dussumieri (Aldabra giant tortoise)
Tissue: red blood cell / References: UniProt: P83133
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 385 / 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: 2.73 Å3/Da / Density % sol: 54.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 7% PEG 3350, 50mM HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU ULTRAX 18 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 8, 2005
RadiationMonochromator: confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.86→53.51 Å / Num. obs: 28249 / % possible obs: 96 % / Redundancy: 3.76 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.035
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 3.74 % / Rmerge(I) obs: 0.138 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNX2005refinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
CNXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V75

1v75


Resolution: 1.86→30.57 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 722671.65 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.217 2805 9.9 %RANDOM
Rwork0.185 ---
obs-28243 95.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.5897 Å2 / ksol: 0.361074 e/Å3
Displacement parametersBiso mean: 31.8 Å2
Baniso -1Baniso -2Baniso -3
1--4.85 Å20 Å2-0.47 Å2
2--11.1 Å20 Å2
3----6.26 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 1.86→30.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 90 385 2767
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.6
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 500 10.8 %
Rwork0.296 4143 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3hem_xplor.paramhem_xplor.top
X-RAY DIFFRACTION4cmo_xplor.paramcmo_xplor.top
X-RAY DIFFRACTION5ion.paramion.top

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