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- PDB-6f17: Structure of Mb NMH H64V, V68A mutant resting state -

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Basic information

Entry
Database: PDB / ID: 6f17
TitleStructure of Mb NMH H64V, V68A mutant resting state
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
PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8272
Polymers18,2111
Non-polymers6161
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1140 Å2
ΔGint-18 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.592, 47.259, 76.200
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-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 1.96 Å3/Da / Density % sol: 37.16 %
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: 1.45→40.2 Å / Num. obs: 25715 / % possible obs: 98.9 % / Redundancy: 6.2 % / CC1/2: 1 / Rmerge(I) obs: 0.043 / Net I/σ(I): 19.3
Reflection shellResolution: 1.45→1.47 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.571 / Mean I/σ(I) obs: 2.6 / CC1/2: 0.903 / % possible all: 96.4

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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: 1.45→40.162 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2168 1997 7.79 %
Rwork0.184 --
obs0.1866 25646 98.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.45→40.162 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 43 176 1431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011306
X-RAY DIFFRACTIONf_angle_d0.9941772
X-RAY DIFFRACTIONf_dihedral_angle_d17.754476
X-RAY DIFFRACTIONf_chiral_restr0.067184
X-RAY DIFFRACTIONf_plane_restr0.005219
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.45-1.48630.23421360.2381618X-RAY DIFFRACTION96
1.4863-1.52650.28781390.22621634X-RAY DIFFRACTION97
1.5265-1.57140.26151390.21761652X-RAY DIFFRACTION98
1.5714-1.62210.27421410.21551670X-RAY DIFFRACTION98
1.6221-1.68010.2611400.21161667X-RAY DIFFRACTION99
1.6801-1.74730.26111410.20211676X-RAY DIFFRACTION99
1.7473-1.82690.24961430.19971680X-RAY DIFFRACTION99
1.8269-1.92320.23981420.19051676X-RAY DIFFRACTION99
1.9232-2.04370.23221440.18291708X-RAY DIFFRACTION99
2.0437-2.20150.20881430.17431691X-RAY DIFFRACTION99
2.2015-2.4230.21591410.18681673X-RAY DIFFRACTION98
2.423-2.77350.23371460.19071727X-RAY DIFFRACTION99
2.7735-3.4940.20851450.181722X-RAY DIFFRACTION99
3.494-40.17740.17721570.16291855X-RAY DIFFRACTION100

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