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- PDB-2eb9: Crystal Structure of Cu(II)(Sal-Leu)/apo-Myoglobin -

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Basic information

Entry
Database: PDB / ID: 2eb9
TitleCrystal Structure of Cu(II)(Sal-Leu)/apo-Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / OXYGEN STORAGE-TRANSPORT complex
Function / homology
Function and homology information


hydrogen peroxide mediated signaling pathway / 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
(N-SALICYLIDEN-L-LEUCINATO)-COPPER(II) / PHOSPHATE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 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: Non-polymer description / 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2308
Polymers17,3661
Non-polymers8647
Water2,234124
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.580, 57.901, 75.282
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 / Phosphate


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-CUS / (N-SALICYLIDEN-L-LEUCINATO)-COPPER(II)


Mass: 296.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H15CuNO3
#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.: 124 / 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: 2.04 Å3/Da / Density % sol: 39.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: 1.37M 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: Feb 6, 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→50 Å / Num. obs: 13338 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Redundancy: 9.7 % / Biso Wilson estimate: 25.186 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 37.87
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.266 / % possible all: 92.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1V9Q
Resolution: 1.8→23.03 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.922 / SU B: 3.053 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.153 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23948 678 5.1 %RANDOM
Rwork0.18923 ---
obs0.19162 12641 96.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.314 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.8→23.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 49 124 1367
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221270
X-RAY DIFFRACTIONr_angle_refined_deg1.4771.9961710
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7285150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.19824.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.57515234
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.062154
X-RAY DIFFRACTIONr_chiral_restr0.1010.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02912
X-RAY DIFFRACTIONr_nbd_refined0.2110.2659
X-RAY DIFFRACTIONr_nbtor_refined0.3060.2843
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.284
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2420.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.224
X-RAY DIFFRACTIONr_mcbond_it0.9131.5769
X-RAY DIFFRACTIONr_mcangle_it1.48421187
X-RAY DIFFRACTIONr_scbond_it2.6953561
X-RAY DIFFRACTIONr_scangle_it4.1664.5521
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 56 -
Rwork0.267 817 -
obs--89.63 %

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