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- PDB-1v75: Crystal structure of hemoglobin D from the Aldabra giant tortoise... -

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Basic information

Entry
Database: PDB / ID: 1v75
TitleCrystal structure of hemoglobin D from the Aldabra giant tortoise (Geochelone gigantea) at 2.0 A resolution
Components
  • Hemoglobin A and D beta chain
  • Hemoglobin D alpha chain
KeywordsOXYGEN STORAGE/TRANSPORT / HEMOGLOBIN D / REPTILIA / THE ALDABRA GIANT TORTOISE / GEOCHELONE GIGANTEA / OXYGEN STORAGE-TRANSPORT COMPLEX
Function / homology
Function and homology information


hemoglobin complex / oxygen carrier activity / oxygen binding / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
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: 2.02 Å
AuthorsKuwada, T. / Hasegawa, T. / Satoh, I. / Ishikawa, K. / Shishikura, F.
CitationJournal: Protein Pept.Lett. / Year: 2003
Title: Crystallization and preliminary X-ray diffraction study of hemoglobin D from the Aldabra giant tortoise, Geochelone gigantea.
Authors: Kuwada, T. / Hasegawa, T. / Satoh, I. / Ishikawa, K. / Shishikura, F.
History
DepositionDec 12, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 9, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_conn.ptnr2_label_seq_id / _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 alpha chain
B: Hemoglobin A and D beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6184
Polymers32,3852
Non-polymers1,2332
Water7,422412
1
A: Hemoglobin D alpha chain
B: Hemoglobin A and D beta chain
hetero molecules

A: Hemoglobin D alpha chain
B: Hemoglobin A and D beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,2368
Polymers64,7704
Non-polymers2,4664
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Unit cell
Length a, b, c (Å)112.142, 62.374, 53.980
Angle α, β, γ (deg.)90.00, 110.26, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-425-

HOH

21B-321-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -x, y, -z.

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Components

#1: Protein Hemoglobin D alpha chain / hemoglobin alpha-D 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 and D beta chain / hemoglobin 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 / Heme B


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


Mass: 18.015 Da / Num. of mol.: 412 / 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: 2.33 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG3350, 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: Oct 15, 2002
RadiationMonochromator: Conforcal Max-Flux / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.02→53.65 Å / Num. obs: 22787 / % possible obs: 98.8 % / Redundancy: 2.78 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 11.8
Reflection shellResolution: 2.02→2.09 Å / Redundancy: 2.71 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
CNX2000.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNX2000.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→33.96 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 411817.34 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.233 2260 9.9 %RANDOM
Rwork0.188 ---
obs-22778 98.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 91.5651 Å2 / ksol: 0.400326 e/Å3
Displacement parametersBiso mean: 35.2 Å2
Baniso -1Baniso -2Baniso -3
1--6.85 Å20 Å2-0.71 Å2
2--16.59 Å20 Å2
3----9.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.02→33.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2212 0 86 412 2710
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d16
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.71
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: 2.02→2.15 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.263 388 10.2 %
Rwork0.261 3419 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4HEM2.PARAMHEM2.TOP

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