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- PDB-2eb8: Crystal Structure of Cu(II)(Sal-Phe)/apo-Myoglobin -

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Basic information

Entry
Database: PDB / ID: 2eb8
TitleCrystal Structure of Cu(II)(Sal-Phe)/apo-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
(N-SALICYLIDEN-L-PHENYLALANATO)-COPPER(II) / PHOSPHATE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAbe, S. / Okazaki, S. / Ueno, T. / Hikage, T. / Suzuki, A. / Yamane, T. / Watanabe, Y.
CitationJournal: Inorg.Chem. / Year: 2007
Title: Design and Structure Analysis of Artificial Metalloproteins: Selective Coordination of His64 to Copper Complexes with Square-Planar Structure in the apo-Myoglobin Scaffold
Authors: Abe, S. / Ueno, T. / Reddy, P.A.N. / Okazaki, S. / Hikage, T. / Suzuki, A. / Yamane, T. / Nakajima, H. / Watanabe, Y.
History
DepositionFeb 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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
Remark 650HELIX Determination method: Author determined

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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)18,1727
Polymers17,3661
Non-polymers8066
Water2,450136
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.691, 59.132, 74.188
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: 17366.148 Da / Num. of mol.: 1
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.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CUP / (N-SALICYLIDEN-L-PHENYLALANATO)-COPPER(II)


Mass: 330.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H13CuNO3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 136 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.3M 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: Jul 29, 2005
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. obs: 17781 / % possible obs: 98.8 % / Observed criterion σ(I): 0 / Redundancy: 9.4 % / Biso Wilson estimate: 21.168 Å2 / Rmerge(I) obs: 0.092 / Net I/σ(I): 40.59
Reflection shellResolution: 1.65→1.71 Å / Rmerge(I) obs: 0.293 / % possible all: 96.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V9Q

1v9q


Resolution: 1.65→26.7 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.929 / SU B: 2.062 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24636 906 5.1 %RANDOM
Rwork0.2034 ---
obs0.20546 16850 98.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.433 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.65→26.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 0 46 136 1422
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221315
X-RAY DIFFRACTIONr_angle_refined_deg1.4831.9941776
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5435159
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.424.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.20315246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.889154
X-RAY DIFFRACTIONr_chiral_restr0.0890.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02953
X-RAY DIFFRACTIONr_nbd_refined0.2160.2640
X-RAY DIFFRACTIONr_nbtor_refined0.3110.2873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.299
X-RAY DIFFRACTIONr_metal_ion_refined0.1020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.218
X-RAY DIFFRACTIONr_mcbond_it0.9691.5789
X-RAY DIFFRACTIONr_mcangle_it1.63721234
X-RAY DIFFRACTIONr_scbond_it2.6843578
X-RAY DIFFRACTIONr_scangle_it4.2894.5538
X-RAY DIFFRACTIONr_sphericity_bonded7.6131
LS refinement shellResolution: 1.649→1.692 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 80 -
Rwork0.286 1146 -
obs--94.45 %

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