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- PDB-5o41: Low-dose fixed target serial synchrotron crystallography structur... -

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Basic information

Entry
Database: PDB / ID: 5o41
TitleLow-dose fixed target serial synchrotron crystallography structure of sperm whale myoglobin
ComponentsMyoglobin
KeywordsOXYGEN BINDING / oxygen storage
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsOwen, R.L. / Axford, D. / Sherrell, D. / Mueller-Werkmeister, H.
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2017
Title: Low-dose fixed-target serial synchrotron crystallography.
Authors: Owen, R.L. / Axford, D. / Sherrell, D.A. / Kuo, A. / Ernst, O.P. / Schulz, E.C. / Miller, R.J. / Mueller-Werkmeister, H.M.
History
DepositionMay 25, 2017Deposition site: PDBE / Processing site: PDBE
SupersessionJun 14, 2017ID: 5M3R
Revision 1.0Jun 14, 2017Provider: 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 / database_2 / pdbx_initial_refinement_model
Item: _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)18,2025
Polymers17,3651
Non-polymers8374
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-41 kcal/mol
Surface area8070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.873, 46.876, 84.665
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: 17365.164 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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.16 Å3/Da / Density % sol: 43.16 %
Crystal growTemperature: 293 K / Method: small tubes / Details: Tris, HCl, ammonium sulfate, CO

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.8→42.35 Å / Num. obs: 14552 / % possible obs: 100 % / Redundancy: 25.3 % / CC1/2: 0.936 / Rmerge(I) obs: 0.7947 / Net I/σ(I): 4.27
Reflection shellResolution: 1.8→1.83 Å / Redundancy: 18.3 % / Rmerge(I) obs: 0.9256 / Mean I/σ(I) obs: 0.36 / CC1/2: 0.475 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
DIALSdata reduction
cctbx.primedata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a6m

1a6m


Resolution: 1.8→42.333 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.47
RfactorNum. reflection% reflection
Rfree0.2532 1454 10 %
Rwork0.1948 --
obs0.2006 14539 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.8→42.333 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 55 171 1451
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0171356
X-RAY DIFFRACTIONf_angle_d1.3241840
X-RAY DIFFRACTIONf_dihedral_angle_d8.1061087
X-RAY DIFFRACTIONf_chiral_restr0.065190
X-RAY DIFFRACTIONf_plane_restr0.009228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.86440.3441410.31311272X-RAY DIFFRACTION99
1.8644-1.9390.32721430.26011284X-RAY DIFFRACTION100
1.939-2.02720.28671410.23551278X-RAY DIFFRACTION100
2.0272-2.13410.29311430.21271284X-RAY DIFFRACTION100
2.1341-2.26780.26931440.20421293X-RAY DIFFRACTION100
2.2678-2.44290.25371440.18881298X-RAY DIFFRACTION100
2.4429-2.68870.2611470.18131313X-RAY DIFFRACTION100
2.6887-3.07770.23311460.1741314X-RAY DIFFRACTION100
3.0777-3.87710.22041470.15641338X-RAY DIFFRACTION100
3.8771-42.34440.21471580.17851411X-RAY DIFFRACTION100

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