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- PDB-1j3f: Crystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me... -

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Basic information

Entry
Database: PDB / ID: 1j3f
TitleCrystal Structure of an Artificial Metalloprotein:Cr(III)(3,3'-Me2-salophen)/apo-A71G Myoglobin
ComponentsMyoglobin
KeywordsOXYGEN STORAGE/TRANSPORT / myoglobin / asymmetric catalysis / crystal / Schiff bases / chromium / 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
CHROMIUM ION / Chem-CZM / PHOSPHATE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.45 Å
AuthorsKoshiyama, T. / Kono, M. / Ohashi, M. / Ueno, T. / Suzuki, A. / Yamane, T. / Watanabe, Y.
Citation
Journal: J.Am.Chem.Soc. / Year: 2005
Title: Coordinated Design of Cofactor and Active Site Structures in Development of New Protein Catalysts
Authors: Ueno, T. / Koshiyama, T. / Ohashi, M. / Kondo, K. / Kono, M. / Suzuki, A. / Yamane, T. / Watanabe, Y.
#1: Journal: Inorg.Chem. / Year: 2004
Title: Crystal Structures of Artificial Metalloproteins: Tight Binding of Fe(III)(Schiff-Base) by Mutation of Ala71 to Gly in Apo-Myoglobin.
Authors: Ueno, T. / Ohashi, M. / Kono, M. / Kondo, K. / Suzuki, A. / Yamane, T. / Watanabe, Y.
History
DepositionJan 24, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 18, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)18,3189
Polymers17,3521
Non-polymers9668
Water4,846269
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.972, 58.787, 76.237
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: TB-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-CR / CHROMIUM ION


Mass: 51.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cr
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-CZM / 'N,N'-BIS-(2-HYDROXY-3-METHYL-BENZYLIDENE)-BENZENE-1,2-DIAMINE' / 3,3'-ME2-SALOPHEN


Mass: 344.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H20N2O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / 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: 1.72 Å3/Da / Density % sol: 28.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: sodium, potassium phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 31, 2002
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.45→40 Å / Num. all: 26654 / Num. obs: 26426 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 18.3 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 40.6
Reflection shellResolution: 1.45→1.5 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 9.9 / % possible all: 90

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1BVC

1bvc


Resolution: 1.45→30.26 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1798486.43 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.219 1251 4.8 %RANDOM
Rwork0.194 ---
all0.196 26266 --
obs0.194 25855 95.6 %-
Refine analyzeLuzzati coordinate error obs: 0.17 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.11 Å
Refinement stepCycle: LAST / Resolution: 1.45→30.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 57 269 1531
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.8
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION4DNA-RNA_REP.PARAMPROTEIN_BREAK.TOP
X-RAY DIFFRACTION5CZM.PARAMCZM.TOP

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