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- PDB-7e43: Structural insights into a bifunctional peptide methionine sulfox... -

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Basic information

Entry
Database: PDB / ID: 7.0E+43
TitleStructural insights into a bifunctional peptide methionine sulfoxide reductase MsrA/B fusion protein from Helicobacter pylori
ComponentsPeptide methionine sulfoxide reductase MsrA/MsrB
KeywordsOXIDOREDUCTASE / MsrAB / fusion protein / linker region
Function / homology
Function and homology information


L-methionine (S)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / protein modification process / response to oxidative stress
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Mss4-like superfamily
Similarity search - Domain/homology
ACETATE ION / Peptide methionine sulfoxide reductase MsrA/MsrB
Similarity search - Component
Biological speciesHelicobacter pylori 26695 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKim, S. / Lee, K. / Hwang, K.Y.
CitationJournal: Antioxidants (Basel) / Year: 2021
Title: Structural Insights into a Bifunctional Peptide Methionine Sulfoxide Reductase MsrA/B Fusion Protein from Helicobacter pylori .
Authors: Kim, S. / Lee, K. / Park, S.H. / Kwak, G.H. / Kim, M.S. / Kim, H.Y. / Hwang, K.Y.
History
DepositionFeb 10, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 21, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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
B: Peptide methionine sulfoxide reductase MsrA/MsrB
A: Peptide methionine sulfoxide reductase MsrA/MsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,8566
Polymers82,6192
Non-polymers2364
Water7,891438
1
B: Peptide methionine sulfoxide reductase MsrA/MsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4283
Polymers41,3101
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area220 Å2
ΔGint-1 kcal/mol
Surface area16990 Å2
MethodPISA
2
A: Peptide methionine sulfoxide reductase MsrA/MsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4283
Polymers41,3101
Non-polymers1182
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.125, 72.505, 82.230
Angle α, β, γ (deg.)93.160, 93.800, 111.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Peptide methionine sulfoxide reductase MsrA/MsrB


Mass: 41309.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori 26695 (bacteria) / Strain: 26695 / Gene: msrAB, msrA, HP_0224 / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12
References: UniProt: O25011, peptide-methionine (S)-S-oxide reductase, peptide-methionine (R)-S-oxide reductase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 438 / 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: 3.49 Å3/Da / Density % sol: 64.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate pH 4.6 and 2.0 M sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 11C / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 53424 / % possible obs: 94.1 % / Redundancy: 3.1 % / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.04 / Rrim(I) all: 0.074 / Χ2: 2.566 / Net I/σ(I): 16.4 / Num. measured all: 163323
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.242.30.17924170.9090.1310.2231.52886.6
2.24-2.282.60.1925250.9120.1320.2332.49187.4
2.28-2.322.50.14925120.950.1050.1831.69189.9
2.32-2.372.60.13926200.9570.0960.171.80990.7
2.37-2.422.60.12825730.9740.0890.1561.75791
2.42-2.482.70.12126570.9710.0820.1471.84893.6
2.48-2.542.80.11326160.980.0750.1371.93492.9
2.54-2.612.90.10626920.980.070.1271.96293.9
2.61-2.682.90.09526630.9840.0620.1141.96994.4
2.68-2.7730.0927230.9870.0580.1072.15996.1
2.77-2.873.10.08627510.9880.0550.1022.26195.7
2.87-2.993.20.07927020.990.0490.0932.55996.4
2.99-3.123.30.07227700.9910.0450.0852.70497
3.12-3.293.40.06827880.9910.0420.082.91997.4
3.29-3.493.60.06427850.9930.0390.0743.17698.1
3.49-3.763.50.05627750.9950.0340.0663.25998.1
3.76-4.143.50.05327670.9940.0330.0633.38297.6
4.14-4.733.50.04927820.9940.0310.0583.33797.2
4.73-5.963.50.04627410.9950.0280.0542.94197.3
5.96-303.30.04825650.9930.0310.0573.21590.3

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E0M

3e0m


Resolution: 2.2→27.59 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.26 / Phase error: 22.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2141 2011 3.77 %
Rwork0.188 51398 -
obs0.1889 53409 93.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.95 Å2 / Biso mean: 39.0177 Å2 / Biso min: 12.89 Å2
Refinement stepCycle: final / Resolution: 2.2→27.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5251 0 16 438 5705
Biso mean--35.02 43.97 -
Num. residues----646
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.250.30581360.26193262339884
2.25-2.310.27011300.233401353188
2.31-2.380.27241380.21823552369090
2.38-2.460.24551390.21753621376092
2.46-2.540.21721420.213623376593
2.54-2.650.23951390.21243716385594
2.65-2.770.28191530.21123756390995
2.77-2.910.24911440.20723755389996
2.91-3.090.25441430.2053764390797
3.09-3.330.20571610.19453832399397
3.33-3.670.18211500.18013851400198
3.67-4.20.16211420.16233824396698
4.2-5.280.19171470.15093823397097
5.28-27.590.19861470.17673618376592

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