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- PDB-8bkn: Carboxymyoglobin dark state for comparison with 5 mJ/cm2 time series -

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Basic information

Entry
Database: PDB / ID: 8bkn
TitleCarboxymyoglobin dark state for comparison with 5 mJ/cm2 time series
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / XFEL / SFX / photolysis / pump-probe / Free-electron Laser / Serial Femtosecond Crystallography
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / oxygen transport / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globin family 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 / MOLECULAR REPLACEMENT / Resolution: 1.29 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 9, 2022Deposition 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 area7720 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 / Heme B


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 / Sulfate


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


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#5: Water ChemComp-HOH / water / 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 / Type: OTHER / Wavelength: 1.03 Å
DetectorType: CUSTOM-MADE / 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: 1.29→30.12 Å / Num. obs: 30443 / % possible obs: 99.9 % / Redundancy: 264.9 % / Biso Wilson estimate: 13.86 Å2 / CC star: 0.992 / R split: 0.147 / Net I/σ(I): 5.7
Reflection shellResolution: 1.29→1.32 Å / Num. unique obs: 1976 / CC star: 0.835 / R split: 0.658

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5d5r

5d5r


Resolution: 1.29→30.12 Å / SU ML: 0.1732 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.8649
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2101 2185 7.18 %
Rwork0.1755 28226 -
obs0.1779 30411 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 17.6 Å2
Refinement stepCycle: LAST / Resolution: 1.29→30.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1194 0 55 130 1379
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121280
X-RAY DIFFRACTIONf_angle_d1.02361734
X-RAY DIFFRACTIONf_chiral_restr0.0669178
X-RAY DIFFRACTIONf_plane_restr0.0067214
X-RAY DIFFRACTIONf_dihedral_angle_d14.9363457
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.29-1.320.36711310.34451699X-RAY DIFFRACTION99.08
1.32-1.350.34081370.28681754X-RAY DIFFRACTION99.89
1.35-1.380.28031350.24891739X-RAY DIFFRACTION100
1.38-1.420.26151370.22571780X-RAY DIFFRACTION100
1.42-1.460.2221350.21151755X-RAY DIFFRACTION100
1.46-1.510.21861370.19261740X-RAY DIFFRACTION100
1.51-1.560.22441390.19451755X-RAY DIFFRACTION100
1.56-1.630.23631340.19631755X-RAY DIFFRACTION100
1.63-1.70.22811330.19881750X-RAY DIFFRACTION100
1.7-1.790.23581390.18371766X-RAY DIFFRACTION100
1.79-1.90.17491370.17231769X-RAY DIFFRACTION100
1.9-2.050.211340.16581769X-RAY DIFFRACTION100
2.05-2.250.18311350.1611772X-RAY DIFFRACTION100
2.25-2.580.20751380.16431788X-RAY DIFFRACTION100
2.58-3.250.18421420.16841793X-RAY DIFFRACTION100
3.25-30.120.20051420.14911842X-RAY DIFFRACTION99.5

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