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- PDB-6n02: CO-bound Sperm Whale Myoglobin, room temperature structure, first... -

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Basic information

Entry
Database: PDB / ID: 6n02
TitleCO-bound Sperm Whale Myoglobin, room temperature structure, first 2 degrees of 5 degree total oscillation
ComponentsMyoglobin, CO-bound
KeywordsOXYGEN TRANSPORT / oxygen transporter / myoglobin / TRANSPORT PROTEIN
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: 2 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
DepositionNov 6, 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 / 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, CO-bound
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1074
Polymers17,3661
Non-polymers7413
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
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.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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, CO-bound


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 BL21 (bacteria) / Strain (production host): BL21 / 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.: 29 / 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: 2.03 Å3/Da / Density % sol: 39.37 %
Crystal growTemperature: 295 K / Method: batch mode / Details: 10 mM Tris HCl pH 9.0 and 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 298 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 1.216 Å
DetectorType: DECTRIS EIGER X 1M / Detector: PIXEL / Date: Mar 4, 2018
RadiationMonochromator: W/B4C multilayer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.216 Å / Relative weight: 1
ReflectionResolution: 2→41.455 Å / Num. obs: 10029 / % possible obs: 99.77 % / Redundancy: 17.2 % / CC1/2: 0.992 / Rpim(I) all: 0.08235 / Rrim(I) all: 0.3473 / Net I/σ(I): 8.66
Reflection shellResolution: 2→2.071 Å / Redundancy: 16.5 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 989 / CC1/2: 0.153 / Rpim(I) all: 2.195 / Rrim(I) all: 9.03 / % possible all: 99.7
Serial crystallography sample deliveryDescription: Si microchips / Method: fixed target
Serial crystallography data reductionFrame hits: 8340 / Frames indexed: 3940 / Frames total: 64000

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VXA

1vxa


Resolution: 2→41.455 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 30.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2825 905 4.95 %random
Rwork0.1979 ---
obs0.2019 18280 99.02 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→41.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 7 29 1304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081320
X-RAY DIFFRACTIONf_angle_d0.9691788
X-RAY DIFFRACTIONf_dihedral_angle_d5.221070
X-RAY DIFFRACTIONf_chiral_restr0.055184
X-RAY DIFFRACTIONf_plane_restr0.004221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.12530.37721520.3732872X-RAY DIFFRACTION98
2.1253-2.28940.33711540.32182871X-RAY DIFFRACTION98
2.2894-2.51980.34111510.25322872X-RAY DIFFRACTION99
2.5198-2.88430.27731470.21712941X-RAY DIFFRACTION99
2.8843-3.63360.33211510.18172906X-RAY DIFFRACTION100
3.6336-41.46390.22691500.15242913X-RAY DIFFRACTION100
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)
13.43682.34551.02268.1230.16033.2302-0.00280.1399-0.0285-0.32610.12260.3224-0.11610.1453-0.10610.31350.0458-0.00120.3438-0.01560.2646-8.3727-0.98277.0815
25.58761.52140.19639.08272.0133.4447-0.1162-0.0819-0.65320.0316-0.01090.73810.5676-0.37490.11580.3528-0.02290.00120.39870.06010.455-16.6382-8.296510.75
32.7724-1.2672-1.01084.5768-1.45286.9372-0.029-0.02430.14990.0485-0.02870.0754-0.09360.13670.04410.22920.0042-0.03330.2799-0.01630.3221-6.8595-0.855813.4852
43.84671.3056-2.73465.5447-3.46013.2233-0.4275-0.1231-0.05710.295-0.1035-0.35190.16080.42120.52750.32170.0184-0.0570.264-0.00670.3473-1.08442.520717.6075
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 42 )
2X-RAY DIFFRACTION2chain 'A' and (resid 43 through 78 )
3X-RAY DIFFRACTION3chain 'A' and (resid 79 through 124 )
4X-RAY DIFFRACTION4chain 'A' and (resid 125 through 153 )

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