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- PDB-5yl3: Crystal structure of horse heart myoglobin reconstituted with man... -

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Basic information

Entry
Database: PDB / ID: 5yl3
TitleCrystal structure of horse heart myoglobin reconstituted with manganese porphycene in resting state at pH 8.5
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / GLOBIN FOLD / OXYGEN TRANSPORT / MUSCLES
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / 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
PORPHYCENE CONTAINING MN / Myoglobin
Similarity search - Component
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
Model detailshorse heart myoglobin reconstituted with manganese porphycene
AuthorsOohora, K. / Meichin, H. / Kihira, Y. / Sugimoto, H. / Shiro, Y. / Hayashi, T.
Funding support Japan, 6items
OrganizationGrant numberCountry
Japan Society for the Promotion of ScienceJP15H05804 Japan
Japan Society for the Promotion of ScienceJP15H00873 Japan
Japan Society for the Promotion of ScienceJP16K14036 Japan
Japan Society for the Promotion of ScienceJP16H06045 Japan
Japan Society for the Promotion of ScienceJP16H00837 Japan
Japan Science and TechnologyJPMJPR15S2 Japan
Citation
Journal: J. Am. Chem. Soc. / Year: 2017
Title: Manganese(V) Porphycene Complex Responsible for Inert C-H Bond Hydroxylation in a Myoglobin Matrix.
Authors: Oohora, K. / Meichin, H. / Kihira, Y. / Sugimoto, H. / Shiro, Y. / Hayashi, T.
#1: Journal: 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
DepositionOct 17, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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)18,0235
Polymers17,1151
Non-polymers9084
Water3,063170
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-13 kcal/mol
Surface area7620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.575, 28.706, 62.702
Angle α, β, γ (deg.)90.000, 106.150, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 17114.711 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / Tissue fraction: heart / References: UniProt: P68082
#2: Chemical ChemComp-HNN / PORPHYCENE CONTAINING MN


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


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 170 / 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: 1.75 Å3/Da / Density % sol: 29.57 % / Mosaicity: 1.008 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Hanging drop containing 1.5 M ammonium sulfate, 5 mg/mL of protein, 50 mM Tris-HCl and 5 mM potassium phosphate at pH 8.5 was equilibrated with the reserver solution containing 3.0 M ...Details: Hanging drop containing 1.5 M ammonium sulfate, 5 mg/mL of protein, 50 mM Tris-HCl and 5 mM potassium phosphate at pH 8.5 was equilibrated with the reserver solution containing 3.0 M ammonium sulfate and 100 mM Tris-HCl buffer at pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Dec 10, 2014 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 19335 / % possible obs: 99.6 % / Redundancy: 7 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.029 / Rrim(I) all: 0.078 / Χ2: 0.898 / Net I/σ(I): 11.1 / Num. measured all: 135739
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.5-1.5350.5268840.8510.2490.5840.85993.8
1.53-1.555.90.4989310.8870.2190.5450.79799.6
1.55-1.586.30.4789800.9080.2040.5210.83699.8
1.58-1.626.80.4159580.9420.170.4490.821100
1.62-1.6570.3889610.9460.1570.4190.823100
1.65-1.697.20.3669730.9520.1460.3940.785100
1.69-1.737.30.3229660.9620.1280.3470.781100
1.73-1.787.30.2579450.9770.1020.2770.841100
1.78-1.837.30.2299690.980.0910.2470.831100
1.83-1.897.30.1999660.9850.0790.2140.921100
1.89-1.967.30.1619750.9870.0630.1730.97100
1.96-2.047.40.1279760.9930.050.1360.97199.9
2.04-2.137.40.1129410.9920.0440.121.07399.9
2.13-2.247.30.0959970.9950.0370.1021.096100
2.24-2.387.30.0839720.9960.0320.0891.11699.9
2.38-2.567.40.0759620.9970.0290.081.083100
2.56-2.827.40.0659780.9970.0250.071.02100
2.82-3.237.30.0539940.9970.0210.0570.819100
3.23-4.077.30.0439880.9990.0170.0460.73899.8
4.07-506.80.0410190.9980.0160.0430.70798.5

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
REFMAC5.8.0135refinement
PDB_EXTRACT3.22data extraction
Cootmodel building
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WI8

3wi8


Resolution: 1.5→30 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.945 / SU B: 3.386 / SU ML: 0.062 / SU R Cruickshank DPI: 0.0922 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.093
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2077 937 5.2 %RANDOM
Rwork0.1683 ---
obs0.1704 17192 94.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 49.7 Å2 / Biso mean: 15.996 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å2-0 Å20.12 Å2
2---0.04 Å20 Å2
3----0.15 Å2
Refinement stepCycle: final / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1185 0 58 170 1413
Biso mean--16.73 27.88 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0191274
X-RAY DIFFRACTIONr_bond_other_d0.0030.021232
X-RAY DIFFRACTIONr_angle_refined_deg2.9472.011728
X-RAY DIFFRACTIONr_angle_other_deg1.06532847
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9895150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.8332552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.91615227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.285152
X-RAY DIFFRACTIONr_chiral_restr0.10.2180
X-RAY DIFFRACTIONr_gen_planes_refined0.0140.0211389
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02275
LS refinement shellResolution: 1.5→1.539 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 50 -
Rwork0.255 840 -
all-890 -
obs--65.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.2551-0.0152-0.00940.39290.06320.108-0.02980.010.017-0.02340.00590.00270.0099-0.00510.02390.0176-0.0068-0.00050.0063-0.00060.007112.6056-4.693214.8192
22.5027-0.38510.71943.09744.04695.8964-0.1243-0.0945-0.08990.15110.08680.06230.14510.07650.03750.0467-0.00880.00720.01330.00430.0049.65512.991514.8767
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 151
2X-RAY DIFFRACTION2A201

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