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- PDB-5cn8: Ultrafast dynamics in myoglobin: 0.3 ps time delay -

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Basic information

Entry
Database: PDB / ID: 5cn8
TitleUltrafast dynamics in myoglobin: 0.3 ps time delay
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / serial femtosecond crystallography / time-resolved crystallography / free-electron laser / protein dynamics / carbon monoxide
Function / homology
Function and homology information


Oxidoreductases; Acting on other nitrogenous compounds as donors / nitrite reductase activity / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / oxygen carrier activity / peroxidase activity / oxygen binding / heme binding / 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 speciesEquus caballus (horse)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / FOURIER SYNTHESIS / Resolution: 1.8 Å
AuthorsBarends, T.R.M. / Foucar, L. / Ardevol, A. / Nass, K.J. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. ...Barends, T.R.M. / Foucar, L. / Ardevol, A. / Nass, K.J. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Koefinger, J. / Koglin, J. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I.
CitationJournal: Science / Year: 2015
Title: Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation.
Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J. ...Authors: Barends, T.R. / Foucar, L. / Ardevol, A. / Nass, K. / Aquila, A. / Botha, S. / Doak, R.B. / Falahati, K. / Hartmann, E. / Hilpert, M. / Heinz, M. / Hoffmann, M.C. / Kofinger, J. / Koglin, J.E. / Kovacsova, G. / Liang, M. / Milathianaki, D. / Lemke, H.T. / Reinstein, J. / Roome, C.M. / Shoeman, R.L. / Williams, G.J. / Burghardt, I. / Hummer, G. / Boutet, S. / Schlichting, I.
History
DepositionJul 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 16, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Nov 4, 2015Group: Database references
Revision 1.3Jan 24, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 14, 2018Group: Data collection / Category: diffrn / diffrn_radiation
Item: _diffrn.pdbx_serial_crystal_experiment / _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l
Revision 1.5Jan 10, 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)17,7635
Polymers16,9261
Non-polymers8374
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1510 Å2
ΔGint-37 kcal/mol
Surface area7850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.600, 28.800, 35.600
Angle α, β, γ (deg.)90.00, 106.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin


Mass: 16926.463 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Equus caballus (horse) / References: UniProt: P68082
#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.: 82 / 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: 20000

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Sample preparation

CrystalDensity Matthews: 1.85 Å3/Da / Density % sol: 33.4 %
Crystal growTemperature: 293 K / Method: batch mode / Details: 3.1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: Y
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: CXI / Wavelength: 1.8-1.85
DetectorType: CS-PAD CXI-2 / Detector: PIXEL / Date: Jun 16, 2014
RadiationProtocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.81
21.851
ReflectionResolution: 1.8→15 Å / Num. obs: 11719 / % possible obs: 100 % / Redundancy: 148 % / Net I/σ(I): 3.9
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 74 % / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
CrystFELdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5CMV

5cmv


Resolution: 1.8→14.708 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2153 732 6.25 %RANDOM
Rwork0.1716 ---
obs0.1742 11719 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→14.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 82 1331
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061280
X-RAY DIFFRACTIONf_angle_d1.0071734
X-RAY DIFFRACTIONf_dihedral_angle_d15.719457
X-RAY DIFFRACTIONf_chiral_restr0.034178
X-RAY DIFFRACTIONf_plane_restr0.004214
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.93870.31731590.26192153X-RAY DIFFRACTION100
1.9387-2.13330.24331730.19492129X-RAY DIFFRACTION100
2.1333-2.44070.21411340.16562210X-RAY DIFFRACTION100
2.4407-3.07050.22831370.18472214X-RAY DIFFRACTION100
3.0705-14.70830.18941290.15572281X-RAY DIFFRACTION100

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