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- PDB-3wi8: Crystal structure of horse heart myoglobin reconstituted with man... -

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Basic information

Entry
Database: PDB / ID: 3wi8
TitleCrystal structure of horse heart myoglobin reconstituted with manganese porphycene
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 domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PORPHYCENE CONTAINING MN / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsMizohata, E. / Oohora, K. / Kihira, Y. / Inoue, T. / Hayashi, T.
CitationJournal: J.Am.Chem.Soc. / Year: 2013
Title: C(sp3)-H bond hydroxylation catalyzed by myoglobin reconstituted with manganese porphycene.
Authors: Oohora, K. / Kihira, Y. / Mizohata, E. / Inoue, T. / Hayashi, T.
History
DepositionSep 9, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,7954
Polymers16,9841
Non-polymers8123
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.828, 28.657, 63.744
Angle α, β, γ (deg.)90.00, 105.18, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#2: Chemical ChemComp-HNN / PORPHYCENE CONTAINING MN


Mass: 619.612 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H36MnN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.2M ammonium sulfate, 0.1M imidazole, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: May 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 6299 / % possible obs: 97.8 % / Rsym value: 0.055 / Net I/σ(I): 24.9
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 3.2 / Rsym value: 0.345 / % possible all: 95.5

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Processing

Software
NameVersionClassification
BSSdata collection
PHASERphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→18 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.936 / SU B: 19.338 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25319 292 4.7 %RANDOM
Rwork0.18607 ---
obs0.18904 5939 97.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.519 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.35 Å2
2---0.71 Å20 Å2
3---0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.2→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 53 12 1250
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211279
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.9132.0031736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5155152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.20324.90653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09515228
X-RAY DIFFRACTIONr_dihedral_angle_4_deg26.775152
X-RAY DIFFRACTIONr_chiral_restr0.1210.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021940
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_it0.8031.5747
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.51521189
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4563532
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.9694.5546
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: 2.196→2.252 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 19 -
Rwork0.356 404 -
obs--94.42 %
Refinement TLS params.Method: refined / Origin x: 12.8314 Å / Origin y: -4.6208 Å / Origin z: 15.1383 Å
111213212223313233
T0.0547 Å2-0.0146 Å20.0326 Å2-0.0258 Å20.0138 Å2--0.0609 Å2
L3.9648 °2-0.8628 °20.4249 °2-1.9736 °20.2608 °2--2.9475 °2
S-0.0292 Å °0.0831 Å °0.2253 Å °-0.0976 Å °-0.0419 Å °-0.1068 Å °-0.0912 Å °-0.0942 Å °0.071 Å °

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