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- PDB-8f9h: H64A swMb-MeNO adduct -

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Basic information

Entry
Database: PDB / ID: 8f9h
TitleH64A swMb-MeNO adduct
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Myoglobin / Nitroso / Nitrosomethane / 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 / NITROSOMETHANE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.75 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 23, 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

Downloads & links

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Assembly

Deposited unit
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0564
Polymers17,2981
Non-polymers7583
Water1,53185
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, UV-Vis spectroscopy supported ligand bound swMb-MeNO
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1520 Å2
ΔGint-29 kcal/mol
Surface area7820 Å2
Unit cell
Length a, b, c (Å)34.856, 29.027, 64.263
Angle α, β, γ (deg.)90.000, 105.890, 90.000
Int Tables number4
Space group name H-MP1211

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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-NSM / NITROSOMETHANE


Mass: 45.041 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH3NO / Feature type: SUBJECT OF INVESTIGATION
#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.: 85 / 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: 1.81 Å3/Da / Density % sol: 31.95 %
Crystal growTemperature: 296.3 K / Method: batch mode / pH: 7.4
Details: 2.3-2.6 M Ammonium Sulfate, 100 mM Tris-HCl, 1 mm EDTA, pH 7.4
Temp details: Room temperature, could fluctuate slightly day by day

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Data collection

DiffractionMean temperature: 100 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: Jul 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.75→50.01 Å / Num. obs: 12746 / % possible obs: 99.4 % / Redundancy: 3.8 % / Rpim(I) all: 0.026 / Rrim(I) all: 0.053 / Net I/σ(I): 22.97
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.75-1.7820.0985620.9650.0790.1270.67292.9
1.78-1.812.40.16600.9550.0770.1270.77598.8
1.81-1.852.60.0956160.9760.0690.1180.81699.4
1.85-1.8930.0916160.9780.0610.1110.70699
1.89-1.933.40.0896420.9790.0550.1050.84799.5
1.93-1.973.90.0816280.9840.0470.0940.71299.8
1.97-2.023.90.0856310.9830.0480.0980.868100
2.02-2.0740.0766570.9870.0430.0880.879100
2.07-2.144.20.076130.9860.0380.080.836100
2.14-2.24.20.0626400.9910.0340.0710.74399.8
2.2-2.284.40.0666390.9920.0350.0750.995100
2.28-2.384.40.0586340.9920.0310.0660.69499.8
2.38-2.484.30.0546470.9930.0280.0610.712100
2.48-2.614.40.0526380.9930.0270.0590.721100
2.61-2.784.30.0496310.9940.0260.0550.728100
2.78-2.994.30.0476450.9940.0250.0530.769100
2.99-3.294.30.0426470.9940.0220.0480.78499.8
3.29-3.774.20.0396570.9940.0210.0441.06599.8
3.77-4.7540.0366560.9940.0190.0411.10299.5
4.75-503.40.0276870.9970.0160.0320.78199.7

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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: 1.75→50 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.167 / SU ML: 0.07 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.121 / ESU R Free: 0.119 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.201 619 4.9 %RANDOM
Rwork0.1522 ---
obs0.1545 12074 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 59.27 Å2 / Biso mean: 18.131 Å2 / Biso min: 11.07 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20.01 Å2
2--0.06 Å20 Å2
3---0.01 Å2
Refinement stepCycle: final / Resolution: 1.75→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1198 0 51 85 1334
Biso mean--14.89 22.38 -
Num. residues----151
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191283
X-RAY DIFFRACTIONr_bond_other_d0.0020.021228
X-RAY DIFFRACTIONr_angle_refined_deg2.062.0071735
X-RAY DIFFRACTIONr_angle_other_deg1.08332844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2885150
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83424.23152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.28815233
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.519154
X-RAY DIFFRACTIONr_chiral_restr0.1470.2184
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021394
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02259
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 39 -
Rwork0.204 837 -
all-876 -
obs--95.22 %

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