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- PDB-5fa9: Bifunctional Methionine Sulfoxide Reductase AB (MsrAB) from Trepo... -

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Basic information

Entry
Database: PDB / ID: 5fa9
TitleBifunctional Methionine Sulfoxide Reductase AB (MsrAB) from Treponema denticola
ComponentsPeptide methionine sulfoxide reductase MsrA
KeywordsOXIDOREDUCTASE / Methionine sulfoxide reductase(Msr) / fusion protein / Protein oxidation
Function / homology
Function and homology information


L-methionine:thioredoxin-disulfide S-oxidoreductase activity / 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 => GO:0036211 / 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
(4S,5S)-1,2-DITHIANE-4,5-DIOL / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesTreponema denticola ATCC 35405 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.302 Å
AuthorsHan, A. / Son, J. / Kim, H.-Y. / Hwang, K.Y.
CitationJournal: Biochemistry / Year: 2016
Title: Essential Role of the Linker Region in the Higher Catalytic Efficiency of a Bifunctional MsrA-MsrB Fusion Protein
Authors: Han, A.R. / Kim, M.J. / Kwak, G.H. / Son, J. / Hwang, K.Y. / Kim, H.Y.
History
DepositionDec 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase MsrA
B: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,8919
Polymers73,8152
Non-polymers1,0767
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2860 Å2
ΔGint-17 kcal/mol
Surface area26880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)144.956, 95.584, 81.390
Angle α, β, γ (deg.)90.00, 116.24, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Peptide methionine sulfoxide reductase MsrA / Protein-methionine-S-oxide reductase / Peptide-methionine (S)-S-oxide reductase


Mass: 36907.484 Da / Num. of mol.: 2 / Mutation: C11S, C285S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Treponema denticola ATCC 35405 (bacteria)
Strain: ATCC 35405 / Gene: msrA, TDE_0709 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: Q73PT7, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-D1D / (4S,5S)-1,2-DITHIANE-4,5-DIOL


Mass: 152.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H8O2S2
#3: Chemical
ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 3.43 Å3/Da / Density % sol: 64.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: 0.2 M sodium chloride, 0.1 M sodium potassium phosphate buffer (pH 6.2), 50% polyethylene glycol 200
PH range: 6.0-6.4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 11, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 42971 / % possible obs: 97.26 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 23.2
Reflection shellResolution: 2.3→2.34 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 2.37 / % possible all: 92.7

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data scaling
PHENIXmodel building
MOLREPphasing
Cootrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3E0M

3e0m


Resolution: 2.302→29.634 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.51 / Phase error: 23.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2339 1988 4.63 %
Rwork0.2048 --
obs0.2062 42971 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.302→29.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 0 56 241 5144
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025023
X-RAY DIFFRACTIONf_angle_d0.5716774
X-RAY DIFFRACTIONf_dihedral_angle_d12.7481862
X-RAY DIFFRACTIONf_chiral_restr0.024721
X-RAY DIFFRACTIONf_plane_restr0.002864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3023-2.35990.33041240.30062682X-RAY DIFFRACTION89
2.3599-2.42360.33311480.29432818X-RAY DIFFRACTION94
2.4236-2.49490.34751370.2862842X-RAY DIFFRACTION95
2.4949-2.57540.28951320.25492895X-RAY DIFFRACTION96
2.5754-2.66740.28711440.24142860X-RAY DIFFRACTION96
2.6674-2.77410.2561330.22772907X-RAY DIFFRACTION97
2.7741-2.90030.27141490.22182979X-RAY DIFFRACTION98
2.9003-3.0530.26031470.21422929X-RAY DIFFRACTION99
3.053-3.24410.25321430.21972986X-RAY DIFFRACTION99
3.2441-3.49420.22171390.20872992X-RAY DIFFRACTION99
3.4942-3.84520.22921510.19383001X-RAY DIFFRACTION100
3.8452-4.40.18781430.1622993X-RAY DIFFRACTION100
4.4-5.53770.20371510.1623032X-RAY DIFFRACTION100
5.5377-29.63670.19851470.20243067X-RAY DIFFRACTION100

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