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- PDB-6e02: WT swMb-MeNO -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 600
TitleWT swMb-MeNO
ComponentsMyoglobin
KeywordsOXYGEN STORAGE / Myoglobin / Nitrosomethane
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
PROTOPORPHYRIN IX CONTAINING FE / NITROSOMETHANE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / 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 1.2Oct 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
Revision 1.3Nov 8, 2023Group: Database references / Category: citation / citation_author
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

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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)18,3607
Polymers17,3651
Non-polymers9956
Water5,747319
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-39 kcal/mol
Surface area7980 Å2
Unit cell
Length a, b, c (Å)90.354, 90.354, 45.332
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-567-

HOH

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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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NSM / NITROSOMETHANE


Mass: 45.041 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH3NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 3.08 Å3/Da / Density % sol: 60.01 %
Crystal growTemperature: 298 K / Method: evaporation
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: Nov 22, 2017
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.76→45.33 Å / Num. obs: 21127 / % possible obs: 99.89 % / Redundancy: 7.5 % / Net I/σ(I): 36.21
Reflection shellResolution: 1.76→1.79 Å / Redundancy: 7.48 % / Rmerge(I) obs: 0.174 / Num. unique obs: 2083 / % possible all: 99.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ile

5ile


Resolution: 1.76→45.33 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.491 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.087 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.17188 987 4.7 %RANDOM
Rwork0.13579 ---
obs0.13743 20151 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 13.58 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20.03 Å20 Å2
2--0.07 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 1.76→45.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1217 0 64 319 1600
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0151327
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171239
X-RAY DIFFRACTIONr_angle_refined_deg1.9461.7191799
X-RAY DIFFRACTIONr_angle_other_deg1.21.682886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1495156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.49923.3959
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.89515239
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.812154
X-RAY DIFFRACTIONr_chiral_restr0.0990.2161
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021455
X-RAY DIFFRACTIONr_gen_planes_other0.0080.02254
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_it1.080.914618
X-RAY DIFFRACTIONr_mcbond_other1.0570.912617
X-RAY DIFFRACTIONr_mcangle_it1.5321.361773
X-RAY DIFFRACTIONr_mcangle_other1.5321.364774
X-RAY DIFFRACTIONr_scbond_it2.7811.292709
X-RAY DIFFRACTIONr_scbond_other2.7811.291708
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2391.7831026
X-RAY DIFFRACTIONr_long_range_B_refined7.17715.7331818
X-RAY DIFFRACTIONr_long_range_B_other6.19212.821651
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.76→1.806 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.195 82 -
Rwork0.154 1478 -
obs--98.92 %

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