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- PDB-6mv0: CO-bound Sperm Whale Myoglobin, room temperature structure solved... -

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Basic information

Entry
Database: PDB / ID: 6mv0
TitleCO-bound Sperm Whale Myoglobin, room temperature structure solved by serial 5degree oscillation crystallography
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / oxygen transporter / myoglobin
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-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 speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsFinke, A.D. / Wierman, J.L. / Pare-Labrosse, O. / Sarrachini, A. / Besaw, J. / Mehrabi, P. / Gruner, S.M. / Miller, R.J.D.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM-103485 United States
National Science Foundation (NSF, United States)DMR-1332208 United States
CitationJournal: IUCrJ / Year: 2019
Title: Fixed-target serial oscillation crystallography at room temperature.
Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / ...Authors: Wierman, J.L. / Pare-Labrosse, O. / Sarracini, A. / Besaw, J.E. / Cook, M.J. / Oghbaey, S. / Daoud, H. / Mehrabi, P. / Kriksunov, I. / Kuo, A. / Schuller, D.J. / Smith, S. / Ernst, O.P. / Szebenyi, D.M.E. / Gruner, S.M. / Miller, R.J.D. / Finke, A.D.
History
DepositionOct 24, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_beamline

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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)18,1074
Polymers17,3661
Non-polymers7413
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.030, 45.900, 82.910
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Myoglobin


Mass: 17366.148 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-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 1.96 Å3/Da / Density % sol: 37.28 %
Crystal growTemperature: 298 K / Method: batch mode / pH: 9
Details: 10 mM Tris-HCl pH 9.0 and 3.2 M ammonium sulfate and washed two to three times with the same solution (CO saturated)

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.2155 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018 / Details: Be compound refractive lens
RadiationMonochromator: W/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2155 Å / Relative weight: 1
ReflectionResolution: 1.97→40.16 Å / Num. obs: 10477 / % possible obs: 99.83 % / Redundancy: 22.6 % / Biso Wilson estimate: 42.37 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.2541 / Net I/σ(I): 10.93
Reflection shellResolution: 1.97→2.04 Å / Num. unique obs: 1006 / CC1/2: 0.181 / Rrim(I) all: 0.1648
Serial crystallography sample deliveryDescription: fixed target Si microchips / Method: fixed target
Serial crystallography sample delivery fixed targetDescription: Si microchips / Sample holding: wells / Sample unit size: 20 µm / Support base: goniometer
Serial crystallography data reductionCrystal hits: 2542 / Frame hits: 63550 / Frames indexed: 20750 / Frames total: 160000

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1vxa

1vxa


Resolution: 1.97→40.16 Å / SU ML: 0.311 / Cross valid method: FREE R-VALUE / σ(F): 1.07 / Phase error: 30.6325
RfactorNum. reflection% reflection
Rfree0.2715 945 4.94 %
Rwork0.1985 --
obs0.2019 10472 99.27 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 50.67 Å2
Refinement stepCycle: LAST / Resolution: 1.97→40.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 7 24 1299
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00911308
X-RAY DIFFRACTIONf_angle_d1.23981771
X-RAY DIFFRACTIONf_chiral_restr0.0593183
X-RAY DIFFRACTIONf_plane_restr0.005218
X-RAY DIFFRACTIONf_dihedral_angle_d7.768760
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-2.070.39541330.38662562X-RAY DIFFRACTION97.82
2.07-2.20.38471350.33552566X-RAY DIFFRACTION98.68
2.2-2.370.28741350.2662614X-RAY DIFFRACTION99.57
2.37-2.610.33161400.23572612X-RAY DIFFRACTION99.57
2.61-2.990.28191300.19022608X-RAY DIFFRACTION99.71
2.99-3.770.26041370.17782631X-RAY DIFFRACTION99.93
3.77-40.170.23321350.16262606X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.696351967760.1983309421920.3032452110261.412745364420.6601646409322.313081150960.0303916889250.0851337100974-0.2150286731430.03270198109030.0774876908540.5003073870280.133957551233-0.06473059698710.0001239656231850.357063780616-0.0094780097917-0.04003046084780.3575814071870.01513272149580.387923758393-10.3211147679-4.159858718128.26009794192
21.058980609160.279641621563-0.6401825409450.435515233899-0.4518519126760.728633348190.1048832175010.0522469718996-0.4015200892820.00672456158995-0.0396955768066-0.02466471404820.393277590248-0.178462451416-0.0003582160130080.364926592852-0.00928736816146-0.03834090073540.425531156438-0.001612334273940.546526648461-16.6616939665-4.499367726769.54559146996
31.33038252318-0.06255583127630.300647618761.70800860687-1.088891911011.852960889820.05698530644550.04900135303050.1124184729720.003508696559180.09453934845890.0445149778603-0.2769520995280.0641546020.0006350936610910.3760314580750.023037412640.02702984303130.339783496913-0.007924126679470.3456084517-6.84617055318-0.85887252894413.3993810503
41.14414102915-0.188824428639-0.0645436911331.367064137430.002894976906160.238684095694-0.3983058072410.02491542200710.02201562741840.119760900483-0.113766084302-0.3520728413790.07682363424270.228081887625-0.001767625359870.3803998882170.0204465374646-0.01836671454660.3797448704940.01120801800150.390386027384-1.109474912682.5122713381417.6018674787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 153 )

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