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- PDB-6g5t: Myoglobin H64V/V68A in the resting state, 1.5 Angstrom resolution -

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Basic information

Entry
Database: PDB / ID: 6g5t
TitleMyoglobin H64V/V68A in the resting state, 1.5 Angstrom resolution
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: 1.5 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
DepositionMar 30, 2018Deposition 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)19,0083
Polymers18,3291
Non-polymers6792
Water2,918162
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-17 kcal/mol
Surface area7740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.987, 47.232, 77.026
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: 18329.141 Da / Num. of mol.: 1 / Mutation: H64V,V68A
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 1.98 Å3/Da / Density % sol: 38.01 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M SPG buffer at pH6.8 -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: Nov 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→47.66 Å / Num. obs: 24040 / % possible obs: 99.2 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.04 / Net I/σ(I): 20.2
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.354 / Num. unique obs: 1150 / CC1/2: 0.944 / % possible all: 98.8

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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: 1.5→40.265 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1977 2000 8.35 %
Rwork0.1692 --
obs0.1716 23959 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.5→40.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1223 0 47 162 1432
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061426
X-RAY DIFFRACTIONf_angle_d0.8461949
X-RAY DIFFRACTIONf_dihedral_angle_d19.082532
X-RAY DIFFRACTIONf_chiral_restr0.045200
X-RAY DIFFRACTIONf_plane_restr0.004250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.53750.22311390.19531535X-RAY DIFFRACTION99
1.5375-1.57910.2121410.18751539X-RAY DIFFRACTION100
1.5791-1.62560.19451410.18031551X-RAY DIFFRACTION100
1.6256-1.67810.2041420.18721558X-RAY DIFFRACTION100
1.6781-1.7380.21171400.18321535X-RAY DIFFRACTION100
1.738-1.80760.21491420.18941552X-RAY DIFFRACTION100
1.8076-1.88990.19711420.18651561X-RAY DIFFRACTION100
1.8899-1.98950.2021410.17031543X-RAY DIFFRACTION100
1.9895-2.11420.19581410.16861558X-RAY DIFFRACTION100
2.1142-2.27740.19421430.15851572X-RAY DIFFRACTION100
2.2774-2.50650.19471430.16151572X-RAY DIFFRACTION100
2.5065-2.86920.1921450.17091587X-RAY DIFFRACTION100
2.8692-3.61450.19321470.16081622X-RAY DIFFRACTION100
3.6145-40.27930.19751530.16591674X-RAY DIFFRACTION99

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