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- PDB-4lwm: Crystal structure of methionine sulfoxide reductase U16C/E55D fro... -

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Basic information

Entry
Database: PDB / ID: 4lwm
TitleCrystal structure of methionine sulfoxide reductase U16C/E55D from clostridium oremlandii with methionie sulfoxide
ComponentsPeptide methionine sulfoxide reductase MsrA
KeywordsOXIDOREDUCTASE / ALPHA/BETA FOLD / PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE
Function / homology
Function and homology information


L-methionine:thioredoxin-disulfide S-oxidoreductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein modification process
Similarity search - Function
: / Selenoprotein methionine sulfoxide reductase A, helical domain / Peptide Methionine Sulfoxide Reductase; Chain A / Peptide methionine sulphoxide reductase MsrA / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / S-OXYMETHIONINE / Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.804 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Arch.Biochem.Biophys. / Year: 2014
Title: Structural analysis of 1-Cys type selenoprotein methionine sulfoxide reductase A
Authors: Lee, E.H. / Kwak, G.H. / Kim, M.J. / Kim, H.Y. / Hwang, K.Y.
History
DepositionJul 27, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 2.0Aug 7, 2019Group: Data collection / Database references ...Data collection / Database references / Non-polymer description / Structure summary
Category: chem_comp / entity / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_mutation / _struct_ref_seq_dif.db_mon_id
Revision 2.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0113
Polymers24,7871
Non-polymers2242
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.849, 80.849, 66.921
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-516-

HOH

21A-556-

HOH

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Components

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


Mass: 24786.729 Da / Num. of mol.: 1 / Mutation: (SEC)16C,E55D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii (bacteria) / Strain: OhILAs / Gene: msrA / Plasmid: PET21B / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) STAR
References: UniProt: A8MI53, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-MHO / S-OXYMETHIONINE


Type: L-peptide linking / Mass: 165.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO3S
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.55 Å3/Da / Density % sol: 51.71 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES, 30%(V/V) PEG 5000, 0.2M AMMONIUM SULFATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1.23985
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 30, 2010 / Details: SI(111)
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.23985 Å / Relative weight: 1
ReflectionResolution: 1.8→30 Å / Num. obs: 22944 / % possible obs: 97.1 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 18.4 Å2
Reflection shellResolution: 1.8→1.83 Å / % possible all: 91.5

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX1.8.1_1168refinement
DENZOdata reduction
SCALEPACKdata scaling
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4LWJ

4lwj


Resolution: 1.804→26.464 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8698 / SU ML: 0.24 / σ(F): 0.37 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1184 5.18 %
Rwork0.1791 21693 -
obs0.1814 22877 96.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 69.71 Å2 / Biso mean: 17.1956 Å2 / Biso min: 2.42 Å2
Refinement stepCycle: LAST / Resolution: 1.804→26.464 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1639 0 14 157 1810
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0151686
X-RAY DIFFRACTIONf_angle_d1.4872282
X-RAY DIFFRACTIONf_chiral_restr0.112247
X-RAY DIFFRACTIONf_plane_restr0.007294
X-RAY DIFFRACTIONf_dihedral_angle_d13.659611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.804-1.8860.3571520.2972492264492
1.886-1.98550.28841400.26232621276195
1.9855-2.10980.261600.20662642280296
2.1098-2.27260.19791290.16642718284797
2.2726-2.50120.22611660.15782724289098
2.5012-2.86270.21121500.15342752290299
2.8627-3.60530.20271430.16352817296099
3.6053-26.46690.19221440.16542927307199

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