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- PDB-8f9i: H64A swMb-EtNO adduct -

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Basic information

Entry
Database: PDB / ID: 8f9i
TitleH64A swMb-EtNO adduct
ComponentsMyoglobin
KeywordsTRANSPORT PROTEIN / Myoglobin / Nitroso / Nitrosoethane / RNO / Mb / EtNO
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 domain profile. / Globin / Globin / Globin-like superfamily
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / NITROSOETHANE / Myoglobin
Similarity search - Component
Biological speciesPhyseter catodon (sperm whale)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsHerrera, V.E. / Thomas, L.N.
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
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2359
Polymers34,5962
Non-polymers1,6397
Water5,819323
1
A: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0704
Polymers17,2981
Non-polymers7723
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Myoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1665
Polymers17,2981
Non-polymers8684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.825, 76.772, 50.529
Angle α, β, γ (deg.)90.000, 103.800, 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.: 2 / 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.: 2
Source method: isolated from a genetically manipulated source
Formula: C34H32FeN4O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-NOE / NITROSOETHANE


Mass: 59.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 323 / 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: 2.28 Å3/Da / Density % sol: 45.99 %
Crystal growTemperature: 298 K / Method: batch mode
Details: 2.3-2.6 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: Aug 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 27916 / % possible obs: 97 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.074 / Rpim(I) all: 0.027 / Rrim(I) all: 0.079 / Χ2: 1.758 / Net I/σ(I): 11.7 / Num. measured all: 218057
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.833.70.36112430.9050.2080.4190.82487.5
1.83-1.864.30.35812880.930.1910.4070.90489.8
1.86-1.950.32712830.9490.1580.3640.96489.8
1.9-1.946.10.24713230.9640.1070.271.2592.9
1.94-1.986.70.22613390.9720.0930.2451.08392.3
1.98-2.0370.18413670.9760.0730.1981.2295
2.03-2.087.40.15113740.9890.0580.1621.34496.4
2.08-2.1380.13514100.9910.0510.1451.39498.1
2.13-2.28.20.1314230.9910.0470.1391.30398.8
2.2-2.278.70.13814040.9910.050.1472.207100
2.27-2.358.80.1114530.9950.0390.1171.631100
2.35-2.449.10.09314190.9960.0330.0991.492100
2.44-2.559.30.08514330.9960.030.0911.577100
2.55-2.699.20.08214410.9970.0290.0871.801100
2.69-2.869.30.07514380.9970.0260.0791.604100
2.86-3.089.20.06814420.9970.0230.0712.08100
3.08-3.399.10.05614590.9980.0190.0591.922100
3.39-3.8890.05714330.9980.020.0612.965100
3.88-4.888.70.04914570.9980.0170.0522.67100
4.88-507.90.04214870.9980.0160.0452.64399.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ile

5ile


Resolution: 1.8→41.38 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.92 / SU B: 2.673 / SU ML: 0.085 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.142 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2272 1333 4.8 %RANDOM
Rwork0.1751 ---
obs0.1776 26533 96.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 69.35 Å2 / Biso mean: 17.09 Å2 / Biso min: 8.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.58 Å20 Å20.27 Å2
2---0.34 Å20 Å2
3---0.7 Å2
Refinement stepCycle: final / Resolution: 1.8→41.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 109 323 2872
Biso mean--18.89 25.64 -
Num. residues----308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0132626
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172502
X-RAY DIFFRACTIONr_angle_refined_deg1.6441.6943551
X-RAY DIFFRACTIONr_angle_other_deg1.4711.6155800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.2495.113311
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.82823.421114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.20615476
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.051158
X-RAY DIFFRACTIONr_chiral_restr0.0890.2315
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023008
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02534
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 71 -
Rwork0.228 1754 -
all-1825 -
obs--86.04 %

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