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- PDB-7vuc: Myoglobin mutant L29I/H64G/V68A -

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Basic information

Entry
Database: PDB / ID: 7vuc
TitleMyoglobin mutant L29I/H64G/V68A
ComponentsMyoglobin
KeywordsBIOSYNTHETIC PROTEIN / Artificial / enzyme / myoglobin
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / IMIDAZOLE / Myoglobin
Similarity search - Component
Biological speciesPhyseter macrocephalus (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsTakahashi, K. / Korendovych, I.V. / Tame, J.R.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM119634 United States
CitationJournal: Nature / Year: 2022
Title: NMR-guided directed evolution.
Authors: Bhattacharya, S. / Margheritis, E.G. / Takahashi, K. / Kulesha, A. / D'Souza, A. / Kim, I. / Yoon, J.H. / Tame, J.R.H. / Volkov, A.N. / Makhlynets, O.V. / Korendovych, I.V.
History
DepositionNov 2, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 29, 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)17,9423
Polymers17,2561
Non-polymers6862
Water4,161231
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-20 kcal/mol
Surface area7900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.019, 90.019, 45.368
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Space group name HallP6
Symmetry operation#1: x,y,z
#2: x-y,x,z
#3: y,-x+y,z
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-499-

HOH

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Components

#1: Protein Myoglobin


Mass: 17256.016 Da / Num. of mol.: 1 / Mutation: L29I/H64G/V68A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter macrocephalus (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 231 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.08 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 100mM Tris pH 8, 2.4M ammonium sulphate

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jan 5, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→22.68 Å / Num. obs: 41415 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 7.81 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.027 / Net I/σ(I): 15.5
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 1982 / CC1/2: 0.488 / Rpim(I) all: 0.433

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Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
CrysalisProdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MLU

1mlu


Resolution: 1.4→22.68 Å / SU ML: 0.1148 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.36
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1951 2058 4.97 %
Rwork0.1764 39343 -
obs0.1774 41401 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 12.41 Å2
Refinement stepCycle: LAST / Resolution: 1.4→22.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 48 231 1491
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00541301
X-RAY DIFFRACTIONf_angle_d0.77181761
X-RAY DIFFRACTIONf_chiral_restr0.0602182
X-RAY DIFFRACTIONf_plane_restr0.0051218
X-RAY DIFFRACTIONf_dihedral_angle_d13.8195474
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.26141350.24692538X-RAY DIFFRACTION97.52
1.43-1.470.22621300.22322616X-RAY DIFFRACTION99.71
1.47-1.510.23881230.20212627X-RAY DIFFRACTION100
1.51-1.550.2241520.19362574X-RAY DIFFRACTION99.93
1.55-1.60.21221600.18272593X-RAY DIFFRACTION100
1.6-1.660.1881240.17822631X-RAY DIFFRACTION100
1.66-1.730.19061440.17582599X-RAY DIFFRACTION100
1.73-1.80.16841470.17142632X-RAY DIFFRACTION100
1.8-1.90.18131410.17152608X-RAY DIFFRACTION99.96
1.9-2.020.16881040.16332641X-RAY DIFFRACTION100
2.02-2.170.19451200.15352653X-RAY DIFFRACTION100
2.17-2.390.16731590.16712617X-RAY DIFFRACTION100
2.39-2.740.16461310.16772641X-RAY DIFFRACTION100
2.74-3.450.19071260.17752672X-RAY DIFFRACTION100
3.45-22.680.2191620.17272701X-RAY DIFFRACTION100

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