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- PDB-1wmu: Crystal Structure of Hemoglobin D from the Aldabra Giant Tortoise... -

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Basic information

Entry
Database: PDB / ID: 1wmu
TitleCrystal Structure of Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea, at 1.65 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 family 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: 1.65 Å
AuthorsKuwada, T. / Hasegawa, T. / Satoh, I. / Ishikawa, K. / Shishikura, F.
CitationJournal: To be Published
Title: Crystal Structure of Hemoglobin D from the Aldabra Giant Tortoise, Geochelone gigantea, at 1.65 A resolution
Authors: Kuwada, T. / Hasegawa, T. / Satoh, I. / Ishikawa, K. / Shishikura, F.
History
DepositionJul 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 3, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_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
Water9,188510
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)112.244, 62.138, 53.926
Angle α, β, γ (deg.)90.00, 109.98, 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 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.: 510 / 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: 2.96 Å3/Da / Density % sol: 58.39 %
Crystal growTemperature: 293 K / pH: 7.5 / Details: 50mM Tris-HCl, pH 7.5, temperature 293K

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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, 2003
RadiationMonochromator: confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→40.48 Å / Num. obs: 39802 / % possible obs: 94.7 % / Redundancy: 7.39 % / Biso Wilson estimate: 26.2 Å2 / Rmerge(I) obs: 0.031
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 7.14 % / Rmerge(I) obs: 0.211 / Mean I/σ(I) obs: 5.8 / % possible all: 90.6

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Processing

Software
NameVersionClassification
CNX2000.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
CNX2000.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V75

1v75


Resolution: 1.65→40.48 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1422458.08 / Data cutoff low absF: 0 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4000 10.1 %RANDOM
Rwork0.193 ---
obs-39799 94.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.2267 Å2 / ksol: 0.317773 e/Å3
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1--3.62 Å20 Å2-0.13 Å2
2--8.26 Å20 Å2
3----4.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 1.65→40.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2292 0 86 510 2888
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_d16.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.7
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: 1.65→1.75 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.385 629 9.9 %
Rwork0.365 5699 -
obs--91 %
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 DIFFRACTION4HEM.PARAMHEM.TOP

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