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- PDB-6e03: sperm whale myoglobin nitrosoethane adduct -

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Basic information

Entry
Database: PDB / ID: 6000
Titlesperm whale myoglobin nitrosoethane adduct
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Myoglobin / nitrosoethane / sperm whale
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
PROTOPORPHYRIN IX CONTAINING FE / NITROSOETHANE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / Resolution: 1.76 Å
AuthorsHerrera, V.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biochemistry / Year: 2023
Title: Insights into Nitrosoalkane Binding to Myoglobin Provided by Crystallography of Wild-Type and Distal Pocket Mutant Derivatives.
Authors: Herrera, V.E. / Charles, T.P. / Scott, T.G. / Prather, K.Y. / Nguyen, N.T. / Sohl, C.D. / Thomas, L.M. / Richter-Addo, G.B.
History
DepositionJul 5, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Nov 8, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5569
Polymers17,3651
Non-polymers1,1918
Water2,882160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2300 Å2
ΔGint-83 kcal/mol
Surface area7850 Å2
Unit cell
Length a, b, c (Å)90.272, 90.272, 45.316
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-442-

HOH

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Components

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Protein , 1 types, 1 molecules A

#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 BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P02185

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Non-polymers , 5 types, 168 molecules

#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.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NOE / NITROSOETHANE


Mass: 59.067 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5NO
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 3.07 Å3/Da / Density % sol: 59.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 2.56-3.20 M AS, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4 or 9.0.
PH range: 7.4-9.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Dec 19, 2017
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.76→45.14 Å / Num. obs: 20356 / % possible obs: 96.42 % / Redundancy: 7 % / Net I/σ(I): 16.23
Reflection shellResolution: 1.76→1.79 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
RefinementResolution: 1.76→45.14 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.933 / SU B: 1.789 / SU ML: 0.057 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.095 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19081 960 4.7 %RANDOM
Rwork0.15992 ---
obs0.16134 19411 96.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.689 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20.06 Å20 Å2
2--0.11 Å20 Å2
3----0.36 Å2
Refinement stepCycle: 1 / Resolution: 1.76→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 73 160 1450
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0151326
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171232
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.7281800
X-RAY DIFFRACTIONr_angle_other_deg1.1571.682869
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3075154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.35923.27658
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.65315237
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.928154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2162
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021444
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02252
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_it1.1421.075616
X-RAY DIFFRACTIONr_mcbond_other1.1321.073615
X-RAY DIFFRACTIONr_mcangle_it1.61.601770
X-RAY DIFFRACTIONr_mcangle_other1.61.604771
X-RAY DIFFRACTIONr_scbond_it2.8421.498710
X-RAY DIFFRACTIONr_scbond_other2.841.499711
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1692.1041031
X-RAY DIFFRACTIONr_long_range_B_refined5.51114.6531683
X-RAY DIFFRACTIONr_long_range_B_other5.51314.6581684
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.758→1.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 62 -
Rwork0.242 924 -
obs--62.72 %

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