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- PDB-8f9n: H64A swMb-iPrNO adduct -

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Basic information

Entry
Database: PDB / ID: 8f9n
TitleH64A swMb-iPrNO adduct
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Myoglobin / Nitroso / Nitrosoisopropane / RNO / Mb
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 / Globin / Globin / Globin domain profile. / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / 2-nitrosopropane / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHerrera, V.E. / Thomas, L.M.
Funding support United States, 3items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-1566509 United States
National Science Foundation (NSF, United States)CHE-1213674 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)P20GM103640 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
DepositionNov 24, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release

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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)18,2766
Polymers17,2981
Non-polymers9785
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, UV-Vis spectroscopy supported ligand bound swMb-iPrNO
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1440 Å2
ΔGint-46 kcal/mol
Surface area8080 Å2
Unit cell
Length a, b, c (Å)90.577, 90.577, 45.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number168
Space group name H-MP6
Components on special symmetry positions
IDModelComponents
11A-426-

HOH

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Components

#1: Protein Myoglobin


Mass: 17298.094 Da / Num. of mol.: 1 / Mutation: H64A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Physeter catodon (sperm whale) / Gene: MB / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P02185
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XEP / 2-nitrosopropane


Mass: 73.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H7NO / 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.11 Å3/Da / Density % sol: 60.43 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 2.3 - 2.6 M Ammonium Sulfate, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50.01 Å / Num. obs: 19658 / % possible obs: 97.87 % / Redundancy: 6.1 % / Rrim(I) all: 0.145 / Net I/σ(I): 22.28
Reflection shellResolution: 1.8→1.864 Å / Num. unique obs: 1877 / CC1/2: 0.67 / Rpim(I) all: 0.301 / Rrim(I) all: 0.638

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ile

5ile


Resolution: 1.8→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.428 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2298 929 4.8 %RANDOM
Rwork0.1967 ---
obs0.1983 18593 97.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 72.1 Å2 / Biso mean: 15.777 Å2 / Biso min: 6.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 1.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 0 63 132 1407
Biso mean--18.86 21.12 -
Num. residues----153
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191307
X-RAY DIFFRACTIONr_bond_other_d0.0020.021241
X-RAY DIFFRACTIONr_angle_refined_deg2.1072.0141769
X-RAY DIFFRACTIONr_angle_other_deg1.0992.9922875
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3135152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.08124.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.50515235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.009154
X-RAY DIFFRACTIONr_chiral_restr0.1390.2187
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021416
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02261
LS refinement shellResolution: 1.8→1.846 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.36 45 -
Rwork0.267 1342 -
obs--94.48 %

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