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- PDB-5utd: Sperm whale myoglobin V68A/I107Y with nitrite -

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Basic information

Entry
Database: PDB / ID: 5utd
TitleSperm whale myoglobin V68A/I107Y with nitrite
ComponentsMyoglobin
KeywordsOXYGEN TRANSPORT / Heme / Myoglobin / Nitrite / Nitrosyl / Nitric oxide
Function / homology
Function and homology information


nitrite reductase activity / Oxidoreductases; Acting on other nitrogenous compounds as donors / sarcoplasm / Oxidoreductases; Acting on a peroxide as acceptor; Peroxidases / removal of superoxide radicals / peroxidase activity / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Myoglobin / Globins / Globin family profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITRITE ION / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.78 Å
Model detailsThis stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale ...This stable porphyrin-Fe(?Ea)-nitrosoalkane complex was obtained from the reaction of sperm whale myoglobin ferric H64A and N-hydroxyamphetamine.
AuthorsWang, B. / Thomas, L.M. / Richter-Addo, G.B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE 1213674 United States
CitationJournal: Biochemistry / Year: 2018
Title: Nitrosyl Myoglobins and Their Nitrite Precursors: Crystal Structural and Quantum Mechanics and Molecular Mechanics Theoretical Investigations of Preferred Fe -NO Ligand Orientations in Myoglobin Distal Pockets.
Authors: Wang, B. / Shi, Y. / Tejero, J. / Powell, S.M. / Thomas, L.M. / Gladwin, M.T. / Shiva, S. / Zhang, Y. / Richter-Addo, G.B.
History
DepositionFeb 14, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 28, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Aug 29, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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)18,1935
Polymers17,3881
Non-polymers8054
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)34.840, 29.260, 64.060
Angle α, β, γ (deg.)90.000, 105.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Myoglobin /


Mass: 17388.111 Da / Num. of mol.: 1 / Mutation: V68A, I107Y
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 / Heme B


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-NO2 / NITRITE ION / Nitrite


Mass: 46.005 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: NO2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / 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: 1.84 Å3/Da / Density % sol: 33.18 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop
Details: 0.1 M Tris-HCl, 1 mM EDTA, pH 7.4 2.56 M Ammonium Sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Jun 19, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.78→61.652 Å / Num. all: 10695 / Num. obs: 10695 / % possible obs: 87.4 % / Redundancy: 2.2 % / Rpim(I) all: 0.034 / Rrim(I) all: 0.056 / Rsym value: 0.032 / Net I/av σ(I): 14.2 / Net I/σ(I): 14.7 / Num. measured all: 23849
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRpim(I) allRrim(I) allRsym value% possible all
1.78-1.8720.1235.10.1170.1830.12391.7
1.87-1.982.10.0887.30.0860.1360.08891.3
1.98-2.122.20.0659.50.0660.1050.06590.6
2.12-2.292.20.0579.30.0550.0880.05789.6
2.29-2.512.30.04511.70.0430.070.04588
2.51-2.812.30.03415.60.0360.0590.03486.1
2.81-3.242.40.02422.70.0260.0430.02484.3
3.24-3.972.50.02918.60.0240.0420.02981.5
3.97-5.612.50.02323.60.0220.0370.02378.3
5.61-26.5812.40.01528.60.0190.0320.01571.3

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Processing

Software
NameVersionClassification
CrystalCleardata collection
SCALA3.3.20data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→26.6 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.913 / SU B: 2.917 / SU ML: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.177 / ESU R Free: 0.17
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2467 512 4.8 %RANDOM
Rwork0.1751 ---
obs0.1785 10177 86.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.17 Å2 / Biso mean: 15.107 Å2 / Biso min: 7.46 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.2 Å2
2--0.7 Å2-0 Å2
3----0.7 Å2
Refinement stepCycle: final / Resolution: 1.78→26.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1205 0 54 98 1357
Biso mean--14.02 20.98 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191292
X-RAY DIFFRACTIONr_angle_refined_deg2.0322.0041748
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3755150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.15924.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55615232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.339154
X-RAY DIFFRACTIONr_chiral_restr0.1560.2182
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021952
LS refinement shellResolution: 1.78→1.821 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.289 37 -
Rwork0.276 791 -
all-828 -
obs--90.39 %

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