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- PDB-3wft: Crystal structure of horse heart myoglobin reconstituted with cob... -

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Basic information

Entry
Database: PDB / ID: 3wft
TitleCrystal structure of horse heart myoglobin reconstituted with cobalt(II) tetradehydrocorrin
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / globin fold / muscles
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin-like / Globin / Globin / Globin domain profile. / 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 / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsMizohata, E. / Morita, Y. / Oohora, K. / Hirata, K. / Ohbayashi, J. / Inoue, T. / Hisaeda, Y. / Hayashi, T.
CitationJournal: Chem.Commun.(Camb.) / Year: 2014
Title: Co(II)/Co(I) reduction-induced axial histidine-flipping in myoglobin reconstituted with a cobalt tetradehydrocorrin as a methionine synthase model.
Authors: Hayashi, T. / Morita, Y. / Mizohata, E. / Oohora, K. / Ohbayashi, J. / Inoue, T. / Hisaeda, Y.
History
DepositionJul 23, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 3, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6778
Polymers16,9841
Non-polymers1,6947
Water2,864159
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.975, 28.987, 63.214
Angle α, β, γ (deg.)90.00, 106.14, 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) / References: UniProt: P68082

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Non-polymers , 5 types, 166 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


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


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 159 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsTHE COBALT COMPLEX J1R, J1S ARE CHARACTERIZED BY PENTA-COORDINATE CO IN 2+ OXIDATION STATE, AS ...THE COBALT COMPLEX J1R, J1S ARE CHARACTERIZED BY PENTA-COORDINATE CO IN 2+ OXIDATION STATE, AS CONFIRMED BY UV-VIS AND EPR SPECTROSCOPY. THE FIFTH COORDINATION IS ACHIEVED BY BINDING TO NE2 OF HIS 93. J1R AND J1S ARE IN ALTERNATE CONFORMATIONS OF EACH OTHER.

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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: 1.81 Å3/Da / Density % sol: 32.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1M Tris-HCl, 3.4M ammonium sulfate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.3→50 Å / Num. obs: 28032 / % possible obs: 92.8 % / Redundancy: 2.8 % / Rsym value: 0.041 / Net I/σ(I): 26.9
Reflection shellResolution: 1.3→1.35 Å / Rsym value: 0.222 / % possible all: 90.1

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Processing

Software
NameVersionClassification
SERGUIdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.3→15 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.963 / SU B: 1.952 / SU ML: 0.037 / Cross valid method: THROUGHOUT / ESU R: 0.058 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18294 1397 5 %RANDOM
Rwork0.12599 ---
obs0.12887 26544 92.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.723 Å2
Baniso -1Baniso -2Baniso -3
1-0.95 Å20 Å20.23 Å2
2---0.81 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1199 0 112 159 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0211367
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg3.0632.0691875
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1115156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16625.09453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.53415234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.337152
X-RAY DIFFRACTIONr_chiral_restr0.1640.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021005
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.861.5760
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.86921211
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.7623607
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.554.5662
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr3.17631367
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.301→1.335 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 83 -
Rwork0.164 1864 -
obs--88.5 %
Refinement TLS params.Method: refined / Origin x: 12.8611 Å / Origin y: -4.6035 Å / Origin z: 15.2199 Å
111213212223313233
T0.004 Å2-0.0008 Å2-0.0012 Å2-0.0155 Å20.0013 Å2--0.0155 Å2
L0.0458 °2-0.0008 °2-0.0047 °2-0.0123 °20.0241 °2--0.0942 °2
S-0.0026 Å °0.0053 Å °0.0031 Å °-0.0002 Å °-0.001 Å °0.0011 Å °-0.0037 Å °-0.0053 Å °0.0036 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 153
2X-RAY DIFFRACTION1A1001 - 1007
3X-RAY DIFFRACTION1A1101 - 1259

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