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- PDB-5azr: Crystal structure of aqua-cobalt(III) tetradehydrocorrin in the h... -

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Basic information

Entry
Database: PDB / ID: 5azr
TitleCrystal structure of aqua-cobalt(III) tetradehydrocorrin in the heme pocket of horse heart myoglobin
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / globin fold / muscles / redox protein
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / oxygen transport / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
(1R,19R) cobalt tetradehydrocorrin / (1S,19S) cobalt tetradehydrocorrin / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.2 Å
AuthorsMizohata, E. / Morita, Y. / Oohora, K. / Inoue, T. / Hayashi, T.
Funding support Japan, 1items
OrganizationGrant numberCountry
JSPS KAKENHI15K18487 Japan
CitationJournal: Inorg.Chem. / Year: 2016
Title: Crystal Structures and Coordination Behavior of Aqua- and Cyano-Co(III) Tetradehydrocorrins in the Heme Pocket of Myoglobin
Authors: Morita, Y. / Oohora, K. / Mizohata, E. / Sawada, A. / Kamachi, T. / Yoshizawa, K. / Inoue, T. / Hayashi, T.
History
DepositionOct 21, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 20, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2016Group: Database references
Revision 1.2Feb 26, 2020Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_site / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5857
Polymers16,9841
Non-polymers1,6026
Water2,720151
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area160 Å2
ΔGint-11 kcal/mol
Surface area7680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.786, 28.837, 63.324
Angle α, β, γ (deg.)90.00, 106.17, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myoglobin /


Mass: 16983.514 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Organ: heart / References: UniProt: P68082

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Non-polymers , 5 types, 157 molecules

#2: Chemical ChemComp-J1R / (1R,19R) cobalt tetradehydrocorrin


Mass: 612.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37CoN4O4
#3: Chemical ChemComp-J1S / (1S,19S) cobalt tetradehydrocorrin


Mass: 612.604 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H37CoN4O4
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 1.8 Å3/Da / Density % sol: 31.52 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: ammonium sulfate, Tris-HCl, trehalose

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.2→50 Å / Num. obs: 37167 / % possible obs: 97.6 % / Redundancy: 3.66 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.4
Reflection shellResolution: 1.2→1.24 Å / % possible all: 97.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0131refinement
HKL-2000data reduction
Cootmodel building
PHASERphasing
RefinementResolution: 1.2→50 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.429 / SU ML: 0.029 / Cross valid method: THROUGHOUT / ESU R: 0.039 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16824 1804 4.9 %RANDOM
Rwork0.12141 ---
obs0.12365 35357 97.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 17.273 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20 Å20.4 Å2
2---0.46 Å20 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 1.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 106 151 1456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0330.0191363
X-RAY DIFFRACTIONr_bond_other_d0.0030.021309
X-RAY DIFFRACTIONr_angle_refined_deg3.2482.0631872
X-RAY DIFFRACTIONr_angle_other_deg1.28433022
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.325158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.95325.18554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.33315235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg4.73152
X-RAY DIFFRACTIONr_chiral_restr0.1840.2190
X-RAY DIFFRACTIONr_gen_planes_refined0.0190.021500
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02292
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0281.386617
X-RAY DIFFRACTIONr_mcbond_other1.6841.37616
X-RAY DIFFRACTIONr_mcangle_it2.3862.078771
X-RAY DIFFRACTIONr_mcangle_other2.4172.084772
X-RAY DIFFRACTIONr_scbond_it4.2641.714746
X-RAY DIFFRACTIONr_scbond_other4.2641.714746
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5262.4321099
X-RAY DIFFRACTIONr_long_range_B_refined4.18212.9921808
X-RAY DIFFRACTIONr_long_range_B_other3.69512.5391756
X-RAY DIFFRACTIONr_rigid_bond_restr5.97432672
X-RAY DIFFRACTIONr_sphericity_free27.698530
X-RAY DIFFRACTIONr_sphericity_bonded10.41652755
LS refinement shellResolution: 1.2→1.232 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 121 -
Rwork0.204 2566 -
obs--97.53 %

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