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- PDB-2ef2: Crystal Structure of an Artificial Metalloprotein:Rh(Phebox-Ph)/a... -

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Basic information

Entry
Database: PDB / ID: 2ef2
TitleCrystal Structure of an Artificial Metalloprotein:Rh(Phebox-Ph)/apo-A71G Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / 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 / Globins / Globin-like / Globin / Globin / Globin domain profile. / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PHOSPHATE ION / [2,6-BIS(4-PHENYL)-1,3-OXAZOLIN-2-YL]RHODIUM(III) / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsAbe, S. / Satake, Y. / Okazaki, S. / Ueno, T. / Hikage, T. / Suzuki, A. / Yamane, T. / Nakajima, H. / Watanabe, Y.
CitationJournal: ORGANOMETALLICS / Year: 2007
Title: Incorporation of a Phebox Rhodium Complex into apo-Myoglobin Affords a Stable Organometallic Protein Showing Unprecedented Arrangement of the Complex in the Cavity
Authors: Satake, Y. / Abe, S. / Okazaki, S. / Ban, N. / Hikage, T. / Ueno, T. / Nakajima, H. / Suzuki, A. / Yamane, T. / Nishiyama, H. / Watanabe, Y.
History
DepositionFeb 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 650HELIX Determination method: Author determined

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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)18,1075
Polymers17,3521
Non-polymers7554
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.046, 57.820, 75.426
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myoglobin


Mass: 17352.123 Da / Num. of mol.: 1 / Mutation: A71G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): TB-1 / References: UniProt: P02185
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-RHX / [2,6-BIS(4-PHENYL)-1,3-OXAZOLIN-2-YL]RHODIUM(III) / [2,6-BIS(4-PHENYL-4,5-DIHYDRO-1,3-OXAZOL-2-YL-KAPPAN)PHENYL-KAPPAC~1~]RHODIUM(3+)


Mass: 470.325 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19N2O2Rh
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2.08 Å3/Da / Density % sol: 40.75 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.35M Sodium, Pottasium Phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Jun 26, 2006
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→80 Å / Num. obs: 13570 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 10.9 % / Biso Wilson estimate: 22.865 Å2 / Rmerge(I) obs: 0.057
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 8.1 % / Rmerge(I) obs: 0.293 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VFJ

1vfj


Resolution: 1.8→21.76 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.918 / SU B: 6.709 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.159 / ESU R Free: 0.16 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26421 685 5.1 %RANDOM
Rwork0.1999 ---
obs0.20313 12868 97.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→21.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1215 0 44 113 1372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0211290
X-RAY DIFFRACTIONr_angle_refined_deg1.831.9951743
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.435157
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.15924.52853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.06915238
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.139154
X-RAY DIFFRACTIONr_chiral_restr0.0930.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02947
X-RAY DIFFRACTIONr_nbd_refined0.220.2679
X-RAY DIFFRACTIONr_nbtor_refined0.3090.2867
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1940.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1860.216
X-RAY DIFFRACTIONr_mcbond_it1.051.5786
X-RAY DIFFRACTIONr_mcangle_it1.65621216
X-RAY DIFFRACTIONr_scbond_it2.5663564
X-RAY DIFFRACTIONr_scangle_it3.9644.5524
LS refinement shellResolution: 1.8→1.846 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.377 48 -
Rwork0.223 865 -
obs--92.13 %

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