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- PDB-5jom: X-ray structure of CO-bound sperm whale myoglobin using a fixed t... -

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Basic information

Entry
Database: PDB / ID: 5jom
TitleX-ray structure of CO-bound sperm whale myoglobin using a fixed target crystallography chip
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / fixed target crystallography chip / CO-bound sperm whale myoglobin / XFEL
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
CARBON MONOXIDE / PROTOPORPHYRIN IX CONTAINING FE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / FREE ELECTRON LASER / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsOghbaey, S. / Sarracini, A. / Ginn, H.M. / Pare-Labrosse, O. / Kuo, A. / Marx, A. / Epp, S.W. / Sherrell, D.A. / Eger, B.T. / Zhong, Y. ...Oghbaey, S. / Sarracini, A. / Ginn, H.M. / Pare-Labrosse, O. / Kuo, A. / Marx, A. / Epp, S.W. / Sherrell, D.A. / Eger, B.T. / Zhong, Y. / Loch, R. / Mariani, V. / Alonso-Mori, R. / Nelson, S. / Lemke, H.T. / Owen, R.L. / Pearson, A.R. / Stuart, D.I. / Ernst, O.P. / Mueller-Werkmeister, H.M. / Miller, R.J.D.
Funding support Canada, Germany, United States, 7items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Canada
Max Planck Society Germany
Canadian Institute for Advanced Research Canada
Canada Excellence Research Chair Program Canada
Anne and Max Tanenbaum Chair in Neuroscience at the University of Toronto Canada
People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013)REA grant agreement no. 623994 Germany
Department of Energy (DOE, United States)Contract No. DE-AC02-76SF00515 United States
CitationJournal: Acta Crystallogr D Struct Biol / Year: 2016
Title: Fixed target combined with spectral mapping: approaching 100% hit rates for serial crystallography.
Authors: Oghbaey, S. / Sarracini, A. / Ginn, H.M. / Pare-Labrosse, O. / Kuo, A. / Marx, A. / Epp, S.W. / Sherrell, D.A. / Eger, B.T. / Zhong, Y. / Loch, R. / Mariani, V. / Alonso-Mori, R. / Nelson, S. ...Authors: Oghbaey, S. / Sarracini, A. / Ginn, H.M. / Pare-Labrosse, O. / Kuo, A. / Marx, A. / Epp, S.W. / Sherrell, D.A. / Eger, B.T. / Zhong, Y. / Loch, R. / Mariani, V. / Alonso-Mori, R. / Nelson, S. / Lemke, H.T. / Owen, R.L. / Pearson, A.R. / Stuart, D.I. / Ernst, O.P. / Mueller-Werkmeister, H.M. / Miller, R.J.
History
DepositionMay 2, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 17, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_oper_list
Item: _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.classification
Revision 1.3Feb 14, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site
Revision 1.4Apr 18, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.5Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_radiation_wavelength / 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)18,1064
Polymers17,3651
Non-polymers7413
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-34 kcal/mol
Surface area8020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.130, 46.483, 84.521
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / 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.: 20 / 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: 2.18 Å3/Da / Density % sol: 43.5 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 9 / Details: 10 mM Tris-HCl, pH 9.0, 2.2-2.5 M ammonium sulfate

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: FREE ELECTRON LASER / Site: SLAC LCLS / Beamline: XPP / Wavelength: 1.293 Å
DetectorType: RAYONIX MX170-HS / Detector: CCD / Date: Mar 20, 2015
RadiationMonochromator: diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.293 Å / Relative weight: 1
ReflectionResolution: 1.9→33.43 Å / Num. obs: 12354 / % possible obs: 100 % / Redundancy: 51.6 % / CC1/2: 0.996 / Net I/σ(I): 6
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
Cheetahdata collection
DIALSdata scaling
CPPXFELdata processing
CPPXFELdata reduction
CPPXFELdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VXA

1vxa


Resolution: 1.9→33.43 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.94 / SU B: 5.057 / SU ML: 0.144 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.259 602 4.9 %RANDOM
Rwork0.21169 ---
obs0.21402 11780 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.726 Å2
Baniso -1Baniso -2Baniso -3
1-0.66 Å20 Å20 Å2
2---0.34 Å20 Å2
3----0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.9→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1225 0 50 20 1295
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0191308
X-RAY DIFFRACTIONr_bond_other_d0.0020.021281
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.0041771
X-RAY DIFFRACTIONr_angle_other_deg0.98732951
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6845153
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57324.25954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.59915239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.083154
X-RAY DIFFRACTIONr_chiral_restr0.1310.2186
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021443
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02301
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9313.531616
X-RAY DIFFRACTIONr_mcbond_other2.8773.532614
X-RAY DIFFRACTIONr_mcangle_it3.7535.296767
X-RAY DIFFRACTIONr_mcangle_other3.7515.296768
X-RAY DIFFRACTIONr_scbond_it4.2994.132692
X-RAY DIFFRACTIONr_scbond_other4.2844.119686
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.5975.91998
X-RAY DIFFRACTIONr_long_range_B_refined7.43628.6331516
X-RAY DIFFRACTIONr_long_range_B_other7.43428.6321516
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.37 43 -
Rwork0.344 844 -
obs--100 %

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