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- PDB-6f19: Structure of Mb NMH H64V, V68A mutant complex with EDA incubated ... -

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Basic information

Entry
Database: PDB / ID: 6f19
TitleStructure of Mb NMH H64V, V68A mutant complex with EDA incubated at room temperature for 5 min
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Myoglobin / Heme / N-methylhistidine
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
ETHYL ACETATE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsTinzl, M. / Hayashi, T. / Mori, T. / Hilvert, D.
CitationJournal: Nat Catal / Year: 2018
Title: Capture and characterization of a reactive haem-carbenoid complex in an artificial metalloenzyme
Authors: Hayashi, T. / Tinzl, M. / Mori, T. / Krengel, U. / Proppe, J. / Soetbeer, J. / Klose, D. / Jeschke, G. / Reiher, M. / Hilvert, D.
History
DepositionNov 21, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)18,9163
Polymers18,2111
Non-polymers7052
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-16 kcal/mol
Surface area7660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.810, 47.770, 77.390
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: 18210.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli (E. coli) / References: UniProt: P02185
#2: Chemical ChemComp-EEE / ETHYL ACETATE


Mass: 88.105 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.02 Å3/Da / Density % sol: 39.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG buffer at pH 6.8-7.2 containing 28-32%(w/v) PEG1500.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.895→50 Å / Num. obs: 11935 / % possible obs: 97.6 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.6
Reflection shellResolution: 1.895→2.01 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 4.5 / CC1/2: 0.934 / % possible all: 93.3

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1A6K

1a6k


Resolution: 1.895→40.65 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2329 1194 10.01 %
Rwork0.1785 --
obs0.1841 11932 97.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→40.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 49 125 1390
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151371
X-RAY DIFFRACTIONf_angle_d1.3371866
X-RAY DIFFRACTIONf_dihedral_angle_d21.604522
X-RAY DIFFRACTIONf_chiral_restr0.08193
X-RAY DIFFRACTIONf_plane_restr0.009231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8955-1.97140.29781200.20681083X-RAY DIFFRACTION92
1.9714-2.06110.26931300.19041161X-RAY DIFFRACTION96
2.0611-2.16980.23151300.17891176X-RAY DIFFRACTION98
2.1698-2.30570.22021310.18311174X-RAY DIFFRACTION98
2.3057-2.48370.28421330.17251196X-RAY DIFFRACTION98
2.4837-2.73360.22691330.18761193X-RAY DIFFRACTION99
2.7336-3.1290.25541340.18231212X-RAY DIFFRACTION99
3.129-3.94170.22281370.16731236X-RAY DIFFRACTION99
3.9417-40.65890.20351460.17591307X-RAY DIFFRACTION99

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