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- PDB-4lwj: Crystal structure of methionine sulfoxide reductase U16C from clo... -

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Basic information

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


L-methionine (S)-S-oxide reductase 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 / Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 2.0Aug 7, 2019Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / struct_conn / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.db_mon_id
Revision 2.1Nov 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 / database_2 / pdbx_initial_refinement_model / 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
Revision 2.2Dec 6, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)24,9723
Polymers24,8171
Non-polymers1552
Water3,873215
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.356, 80.356, 66.942
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-583-

HOH

21A-586-

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: 24816.754 Da / Num. of mol.: 1 / Mutation: (SEC)16(CSO)
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-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 215 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.51 Å3/Da / Density % sol: 51.07 %
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 13, 2009
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→50 Å / Num. obs: 27101 / % possible obs: 98 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 20.97 Å2
Reflection shellResolution: 1.79→1.83 Å / % possible all: 96.5

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Processing

Software
NameVersionClassification
MOLREPphasing
PHENIX(PHENIX.REFINE: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF3

1ff3


Resolution: 1.8→30.87 Å / SU ML: 0.17 / σ(F): 1.56 / Phase error: 17.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1186 5.1 %
Rwork0.18 --
obs0.181 23254 98.8 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.26 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 23.29 Å2
Baniso -1Baniso -2Baniso -3
1-0.3832 Å2-0 Å20 Å2
2--0.3832 Å2-0 Å2
3----0.7664 Å2
Refinement stepCycle: LAST / Resolution: 1.8→30.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1641 0 9 215 1865
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071683
X-RAY DIFFRACTIONf_angle_d1.0162278
X-RAY DIFFRACTIONf_dihedral_angle_d12.917610
X-RAY DIFFRACTIONf_chiral_restr0.076246
X-RAY DIFFRACTIONf_plane_restr0.004292
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.8-1.8820.24141400.1675268998
1.882-1.98120.22631380.1713272198
1.9812-2.10530.23151520.17512740100
2.1053-2.26780.19511600.16412737100
2.2678-2.49590.17411450.1748274999
2.4959-2.85680.23711580.1816271798
2.8568-3.59840.21781590.18822794100
3.5984-30.87820.19621340.1844292199

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