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- PDB-8wf5: Horse heart myoglobin reconstituted with an iron complex of porph... -

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Basic information

Entry
Database: PDB / ID: 8wf5
TitleHorse heart myoglobin reconstituted with an iron complex of porphyrin bearing two CF3 groups (rMb(FePor(CF3)2))
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin
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 / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding ...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 / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / extracellular exosome / metal ion binding
Similarity search - Function
Myoglobin / Globin domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
Biological speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsKagawa, Y. / Oohora, K. / Himiyama, T. / Suzuki, A. / Hayashi, T.
Funding support Japan, 11items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP15H05804 Japan
Japan Society for the Promotion of Science (JSPS)JP18KK0156 Japan
Japan Society for the Promotion of Science (JSPS)JP20H02755 Japan
Japan Society for the Promotion of Science (JSPS)JP20H00403 Japan
Japan Society for the Promotion of Science (JSPS)JP20KK0315 Japan
Japan Society for the Promotion of Science (JSPS)JP22H05364 Japan
Japan Society for the Promotion of Science (JSPS)JP22K21348 Japan
Japan Society for the Promotion of Science (JSPS)JP23H03832 Japan
Japan Science and TechnologyJPMJPR15S2 Japan
Japan Science and TechnologyJPMJPR22A3 Japan
Japan Society for the Promotion of Science (JSPS)JP21J20563 Japan
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Redox Engineering of Myoglobin by Cofactor Substitution to Enhance Cyclopropanation Reactivity.
Authors: Kagawa, Y. / Oohora, K. / Himiyama, T. / Suzuki, A. / Hayashi, T.
History
DepositionSep 19, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release

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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)18,0646
Polymers16,9841
Non-polymers1,0815
Water2,594144
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.260, 28.740, 63.650
Angle α, β, γ (deg.)90.000, 105.472, 90.000
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-WC5 / PROTOPORPHYRIN(CF3)2 CONTAINING FE


Mass: 700.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H26F6FeN4O4 / 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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.83 Å3/Da / Density % sol: 32.79 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.8 M ammonium sulfate, 100 mM Tis-HCl buffer (pH 7.0)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.72→33.792 Å / Num. obs: 12813 / % possible obs: 96.4 % / Redundancy: 6.5 % / CC1/2: 0.991 / Rmerge(I) obs: 0.155 / Net I/σ(I): 10.4
Reflection shellResolution: 1.72→1.75 Å / Rmerge(I) obs: 0.738 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 698 / CC1/2: 0.681
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
REFMAC5.8.0415refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→33.792 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.9 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R: 0.129 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2155 639 4.991 %
Rwork0.1572 12165 -
all0.16 --
obs-12804 95.724 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 19.474 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å20 Å20.006 Å2
2---0.005 Å20 Å2
3----0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.72→33.792 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 68 144 1406
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121292
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161214
X-RAY DIFFRACTIONr_angle_refined_deg1.9731.7251755
X-RAY DIFFRACTIONr_angle_other_deg0.5251.6292813
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2385151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.93452
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.7410229
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.8761053
X-RAY DIFFRACTIONr_chiral_restr0.0710.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02262
X-RAY DIFFRACTIONr_nbd_refined0.2180.2318
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.21098
X-RAY DIFFRACTIONr_nbtor_refined0.1770.2638
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0690.2640
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2240.2102
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1990.220
X-RAY DIFFRACTIONr_nbd_other0.2090.268
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.150.224
X-RAY DIFFRACTIONr_mcbond_it1.7521.819607
X-RAY DIFFRACTIONr_mcbond_other1.7391.818607
X-RAY DIFFRACTIONr_mcangle_it2.7863.252757
X-RAY DIFFRACTIONr_mcangle_other2.7993.261758
X-RAY DIFFRACTIONr_scbond_it2.8392.236685
X-RAY DIFFRACTIONr_scbond_other2.8382.238686
X-RAY DIFFRACTIONr_scangle_it4.3863.903998
X-RAY DIFFRACTIONr_scangle_other4.3843.905999
X-RAY DIFFRACTIONr_lrange_it6.63824.4841626
X-RAY DIFFRACTIONr_lrange_other6.53522.3781580
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.72-1.7650.344520.2279050.2329890.9240.96196.76440.187
1.765-1.8130.26390.2168740.2189390.9520.96497.23110.182
1.813-1.8650.293430.2098360.2139210.9420.96995.43970.171
1.865-1.9220.282610.2058100.2119010.9530.97196.67040.18
1.922-1.9850.257360.198030.1948800.960.97595.34090.161
1.985-2.0550.245390.1767860.1798620.960.97995.70770.155
2.055-2.1320.251330.1737150.1777770.9660.9896.26770.15
2.132-2.2190.246600.1636980.1697980.9630.98294.98750.147
2.219-2.3170.227370.1556840.1597560.9680.98495.37040.135
2.317-2.4290.14350.1496510.1497190.9830.98595.41030.134
2.429-2.560.182290.1446310.1466990.9760.98694.42060.129
2.56-2.7140.192170.1516040.1526520.9710.98595.24540.141
2.714-2.90.232310.1425670.1466170.970.98796.92060.137
2.9-3.1310.175320.1495130.155690.9750.98795.78210.147
3.131-3.4270.265130.1484920.1525260.9580.98596.00760.152
3.427-3.8260.133160.1244470.1244910.9920.99194.29730.131
3.826-4.4090.111130.1183980.1184290.9960.99295.80420.135
4.409-5.3770.226260.1343320.143730.9780.98995.97860.149
5.377-7.510.19150.1882590.1882950.9790.98192.88140.201
7.51-33.7920.233120.1381600.1431810.9740.98795.02760.168

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