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- PDB-3eu1: Crystal Structure determination of goat hemoglobin (Capra hircus)... -

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Basic information

Entry
Database: PDB / ID: 3eu1
TitleCrystal Structure determination of goat hemoglobin (Capra hircus) at 3 angstrom resolution
Components
  • Hemoglobin subunit alpha-1/2
  • Hemoglobin subunit beta-A
KeywordsOxygen storage / Oxygen transport / low oxygen affinity / Capra hircus / hemoglobin / allosteric mechanism / 2 / 3-Diphospho glycerate
Function / homology
Function and homology information


haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / blood microparticle ...haptoglobin binding / hemoglobin alpha binding / haptoglobin-hemoglobin complex / organic acid binding / hemoglobin complex / hydrogen peroxide catabolic process / oxygen carrier activity / peroxidase activity / oxygen binding / 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 / Hemoglobin subunit beta-A / Hemoglobin subunit alpha-1 / Hemoglobin subunit alpha-2
Similarity search - Component
Biological speciesCapra hircus (goat)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsSathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
CitationJournal: Protein Pept.Lett. / Year: 2009
Title: Purification, crystallization and preliminary X-ray diffraction studies on goat (Capra hircus) hemoglobin - a low oxygen affinity species
Authors: Sathya Moorthy, P. / Neelagandan, K. / Balasubramanian, M. / Ponnuswamy, M.N.
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _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 subunit alpha-1/2
B: Hemoglobin subunit beta-A
C: Hemoglobin subunit alpha-1/2
D: Hemoglobin subunit beta-A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6718
Polymers62,2054
Non-polymers2,4664
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11010 Å2
ΔGint-111 kcal/mol
Surface area23970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.678, 66.896, 157.593
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Hemoglobin subunit alpha-1/2 / / Hemoglobin alpha-1/2 chain / Alpha-1/2-globin


Mass: 15056.157 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Cell: RED BLOOD CELLS / Tissue: blood / References: UniProt: P68238, UniProt: P0CH25*PLUS
#2: Protein Hemoglobin subunit beta-A / / Hemoglobin beta-A chain / Beta-A-globin / Alanine beta-globin


Mass: 16046.405 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Capra hircus (goat) / Cell: RED BLOOD CELLS / Tissue: blood / References: UniProt: P02077
#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

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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: 2.27 Å3/Da / Density % sol: 45.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 2micro litres of Hb with 2micro litre of well solution containing 25mM of Phosphate buffer at pH 7.5 with 0.5M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 16, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 10705 / Num. obs: 9607 / % possible obs: 89.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 2 / Redundancy: 4.12 % / Rsym value: 0.1854 / Net I/σ(I): 2.9
Reflection shellResolution: 3→3.11 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 0.7 / Rsym value: 0.5361 / % possible all: 93

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
REFMAC5.2.0019refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3d1a

3d1a


Resolution: 3→22.08 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.835 / SU B: 22.731 / SU ML: 0.405 / Cross valid method: THROUGHOUT / ESU R Free: 0.617 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27796 1036 9.7 %RANDOM
Rwork0.21269 ---
obs0.21906 9607 89.6 %-
all-10705 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 92.55 Å2 / Biso mean: 34.953 Å2 / Biso min: 3.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.02 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 3→22.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4389 0 172 0 4561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0224693
X-RAY DIFFRACTIONr_angle_refined_deg2.0952.0596416
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6825568
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24724.043188
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.72915736
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8991514
X-RAY DIFFRACTIONr_chiral_restr0.1160.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023542
X-RAY DIFFRACTIONr_nbd_refined0.3090.22685
X-RAY DIFFRACTIONr_nbtor_refined0.3260.23124
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2279
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3440.249
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1780.22
X-RAY DIFFRACTIONr_mcbond_it0.8881.52877
X-RAY DIFFRACTIONr_mcangle_it1.26824516
X-RAY DIFFRACTIONr_scbond_it2.03332040
X-RAY DIFFRACTIONr_scangle_it3.0034.51892
LS refinement shellResolution: 3.001→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 79 -
Rwork0.354 696 -
all-775 -
obs--92.04 %

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