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- PDB-8r9f: Multicopy-refined carboxymyoglobin photolysis time series at 23 m... -

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Basic information

Entry
Database: PDB / ID: 8r9f
TitleMulticopy-refined carboxymyoglobin photolysis time series at 23 mJ/cm2 laser fluence, 537 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.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _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
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1500 Å2
ΔGint-36 kcal/mol
Surface area7970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.100, 28.800, 35.800
Angle α, β, γ (deg.)90.000, 106.900, 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.: 112 / 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: 1.87 Å3/Da / Density % sol: 34.15 %
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: Mar 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: 25103 / % possible obs: 99.8 % / Redundancy: 3.6 % / Biso Wilson estimate: 14.32 Å2 / CC star: 0.98 / R split: 0.242 / Net I/σ(I): 3.6
Reflection shellResolution: 1.32→1.35 Å / Num. unique obs: 1925 / CC star: 0.695 / R split: 0.909

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
REFMAC5phasing
CrystFEL0.8.0data reduction
CrystFEL0.8.0data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.4→9.96 Å / SU ML: 0.1175 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2201 1801 7.17 %
Rwork0.1842 23302 -
obs0.1867 25103 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.97 Å2
Refinement stepCycle: LAST / Resolution: 1.4→9.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 112 1361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092560
X-RAY DIFFRACTIONf_angle_d1.07813468
X-RAY DIFFRACTIONf_chiral_restr0.0768356
X-RAY DIFFRACTIONf_plane_restr0.0115428
X-RAY DIFFRACTIONf_dihedral_angle_d15.0712942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.430.27451380.26191729X-RAY DIFFRACTION95.94
1.43-1.480.26131350.23551762X-RAY DIFFRACTION100
1.48-1.520.22681370.22541779X-RAY DIFFRACTION100
1.52-1.580.22051370.20041777X-RAY DIFFRACTION100
1.58-1.640.24251370.19721802X-RAY DIFFRACTION100
1.64-1.710.23421430.19611778X-RAY DIFFRACTION99.95
1.71-1.80.24331380.1871786X-RAY DIFFRACTION100
1.8-1.920.1851340.18281798X-RAY DIFFRACTION100
1.92-2.060.21011420.18671791X-RAY DIFFRACTION100
2.06-2.270.21341370.18031801X-RAY DIFFRACTION100
2.27-2.590.24131390.18381808X-RAY DIFFRACTION100
2.59-3.250.20851420.18471821X-RAY DIFFRACTION100
3.25-9.960.21111420.16291870X-RAY DIFFRACTION100

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