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- PDB-5m3s: Low-dose fixed target serial synchrotron crystallography structur... -

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Basic information

Entry
Database: PDB / ID: 5m3s
TitleLow-dose fixed target serial synchrotron crystallography structure of Metmyoglobin
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 domain profile. / Globin-like / Globin / Globin / 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: 1.8 Å
AuthorsAxford, D. / Owen, R.L. / Sherrell, D. / Muller-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
DepositionOct 17, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 12, 2017Group: Database references
Revision 1.2Apr 19, 2017Group: Database references
Revision 1.3Jan 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,3666
Polymers17,3651
Non-polymers1,0015
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-48 kcal/mol
Surface area8090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.436, 91.436, 45.957
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-205-

SO4

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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: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: SO4 / Source: (gene. exp.) Physeter catodon (sperm whale) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 3.19 Å3/Da / Density % sol: 61.48 %
Crystal growTemperature: 294 K / Method: small tubes / Details: Tris, HCl, ammonium sulfate

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 30, 2016 / Details: KB mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 1.7→39.76 Å / Num. obs: 24300 / % possible obs: 100 % / Redundancy: 75.2 % / CC1/2: 0.9779 / Rmerge(I) obs: 0.7614 / Net I/σ(I): 1.65
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 56.43 % / Rmerge(I) obs: 0.9583 / Mean I/σ(I) obs: 0.23 / CC1/2: 0.5887 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11rc1_2513: ???)refinement
DIALSdata reduction
cctbx.primedata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1a6m

1a6m


Resolution: 1.8→39.748 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 20.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 1689 8.23 %
Rwork0.1798 --
obs0.1834 20519 100 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→39.748 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 63 201 1489
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061340
X-RAY DIFFRACTIONf_angle_d0.8581821
X-RAY DIFFRACTIONf_dihedral_angle_d4.7971382
X-RAY DIFFRACTIONf_chiral_restr0.042187
X-RAY DIFFRACTIONf_plane_restr0.004223
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8530.33191380.33021560X-RAY DIFFRACTION100
1.853-1.91280.33461390.31191548X-RAY DIFFRACTION100
1.9128-1.98120.31431370.27011553X-RAY DIFFRACTION100
1.9812-2.06050.30011440.2421565X-RAY DIFFRACTION100
2.0605-2.15430.26551350.21151534X-RAY DIFFRACTION100
2.1543-2.26780.27231440.19011577X-RAY DIFFRACTION100
2.2678-2.40990.22281450.17361571X-RAY DIFFRACTION100
2.4099-2.59590.19111400.16331557X-RAY DIFFRACTION100
2.5959-2.85710.21481430.15891572X-RAY DIFFRACTION100
2.8571-3.27040.20891360.15671582X-RAY DIFFRACTION100
3.2704-4.11970.17311450.11921582X-RAY DIFFRACTION100
4.1197-39.75750.16651430.14071629X-RAY DIFFRACTION100

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