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- PDB-8r92: Multicopy-refined carboxymyoglobin photolysis time series at 5 mJ... -

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Basic information

Entry
Database: PDB / ID: 8r92
TitleMulticopy-refined carboxymyoglobin photolysis time series at 5 mJ/cm2 laser fluence, 702 fs time delay
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Free-electron laser / time-resolved crystallography / serial crystallography
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 / Globin domain profile. / Globin / Globin / Globin-like superfamily
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: 1.4 Å
AuthorsBarends, T. / Schlichting, I.
Funding support Germany, 1items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nature / Year: 2024
Title: Influence of pump laser fluence on ultrafast myoglobin structural dynamics.
Authors: Barends, T.R.M. / Gorel, A. / Bhattacharyya, S. / Schiro, G. / Bacellar, C. / Cirelli, C. / Colletier, J.P. / Foucar, L. / Grunbein, M.L. / Hartmann, E. / Hilpert, M. / Holton, J.M. / ...Authors: Barends, T.R.M. / Gorel, A. / Bhattacharyya, S. / Schiro, G. / Bacellar, C. / Cirelli, C. / Colletier, J.P. / Foucar, L. / Grunbein, M.L. / Hartmann, E. / Hilpert, M. / Holton, J.M. / Johnson, P.J.M. / Kloos, M. / Knopp, G. / Marekha, B. / Nass, K. / Nass Kovacs, G. / Ozerov, D. / Stricker, M. / Weik, M. / Doak, R.B. / Shoeman, R.L. / Milne, C.J. / Huix-Rotllant, M. / Cammarata, M. / Schlichting, I.
History
DepositionNov 30, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 31, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 21, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Feb 28, 2024Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Mar 6, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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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
Water2,342130
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-36 kcal/mol
Surface area7730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.000, 28.400, 35.300
Angle α, β, γ (deg.)90.000, 107.000, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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 / Feature type: SUBJECT OF INVESTIGATION
#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 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.78 Å3/Da / Density % sol: 31.06 %
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: N
Diffraction sourceSource: FREE ELECTRON LASER / Site: SwissFEL ARAMIS / Beamline: ESB / Wavelength: 1.03 Å
DetectorType: PSI JUNGFRAU 16M / Detector: PIXEL / Date: May 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 1.32→10 Å / Num. obs: 23866 / % possible obs: 99.8 % / Redundancy: 122 % / Biso Wilson estimate: 13.53 Å2 / CC star: 0.982 / R split: 0.223 / Net I/σ(I): 4.1
Reflection shellResolution: 1.32→1.35 Å / Num. unique obs: 1849 / CC star: 0.783 / R split: 0.776

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMACphasing
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→9.95 Å / SU ML: 0.1151 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.6632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2055 1712 7.17 %
Rwork0.175 22154 -
obs0.1771 23866 99.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.65 Å2
Refinement stepCycle: LAST / Resolution: 1.4→9.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 130 1379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01142560
X-RAY DIFFRACTIONf_angle_d1.18763468
X-RAY DIFFRACTIONf_chiral_restr0.0716356
X-RAY DIFFRACTIONf_plane_restr0.0113428
X-RAY DIFFRACTIONf_dihedral_angle_d13.6152942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.440.29151360.24511761X-RAY DIFFRACTION96.25
1.44-1.490.2161460.22361833X-RAY DIFFRACTION100
1.49-1.540.2141390.20631847X-RAY DIFFRACTION100
1.54-1.60.23231480.20471823X-RAY DIFFRACTION100
1.6-1.670.20411390.19881858X-RAY DIFFRACTION100
1.67-1.760.25381460.19081828X-RAY DIFFRACTION100
1.76-1.870.19631400.19221834X-RAY DIFFRACTION100
1.87-2.010.1941390.17921855X-RAY DIFFRACTION100
2.01-2.210.20031420.17261857X-RAY DIFFRACTION100
2.21-2.530.2141450.17061866X-RAY DIFFRACTION100
2.53-3.170.20051470.16871874X-RAY DIFFRACTION100
3.17-9.950.18851450.15051918X-RAY DIFFRACTION100

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