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- PDB-2c0k: The structure of hemoglobin from the botfly Gasterophilus intestinalis -

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Basic information

Entry
Database: PDB / ID: 2c0k
TitleThe structure of hemoglobin from the botfly Gasterophilus intestinalis
ComponentsHEMOGLOBIN
KeywordsOXYGEN TRANSPORT / GASTEROPHILUS INTESTINALIS HEMOGLOBIN / INSECT HEMOGLOBIN / HEME / IRON / METAL-BINDING
Function / homology
Function and homology information


oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin-like, M family globin domain / Globin/Protoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / OXYGEN MOLECULE / Hemoglobin
Similarity search - Component
Biological speciesGASTEROPHILUS INTESTINALIS (fry)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsPesce, A. / Nardini, M. / Dewilde, S. / Hoogewijs, D. / Ascenzi, P. / Moens, L. / Bolognesi, M.
CitationJournal: Protein Sci. / Year: 2005
Title: Modulation of Oxygen Binding to Insect Hemoglobins: The Structure of Hemoglobin from the Botfly Gasterophilus Intestinalis.
Authors: Pesce, A. / Nardini, M. / Dewilde, S. / Hoogewijs, D. / Ascenzi, P. / Moens, L. / Bolognesi, M.
History
DepositionSep 5, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOGLOBIN
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2126
Polymers35,9152
Non-polymers1,2974
Water1086
1
A: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6063
Polymers17,9581
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: HEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6063
Polymers17,9581
Non-polymers6482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.697, 47.697, 145.245
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.17887, 0.98387, -0.00348), (0.98387, 0.17886, -0.00156), (-0.00091, -0.0037, -0.99999)
Vector: 0.11482, 0.07935, 0.34739)

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Components

#1: Protein HEMOGLOBIN


Mass: 17957.660 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) GASTEROPHILUS INTESTINALIS (fry) / References: UniProt: O96457
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.7 Å3/Da / Density % sol: 55 %
Crystal growpH: 7.5 / Details: PEG 4000 25%, 20 MM TRIS PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 4, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→27 Å / Num. obs: 11160 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2BK9

2bk9


Resolution: 2.6→23.85 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.846 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.256 1125 10.1 %RANDOM
Rwork0.186 ---
obs0.193 10033 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.96 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20.01 Å20 Å2
2--0.02 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.6→23.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2461 0 90 6 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222624
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.6992.0293560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5675297
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.81424.015132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.64815457
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1231515
X-RAY DIFFRACTIONr_chiral_restr0.0670.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022012
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.21110
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21741
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.212
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.781.51527
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.36722398
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.07431262
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.224.51158
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.344 73
Rwork0.269 735

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