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- PDB-4w8c: Crystal structure of the helical domain deleted form MsrA from Cl... -

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Basic information

Entry
Database: PDB / ID: 4w8c
TitleCrystal structure of the helical domain deleted form MsrA from Clostridium oremlandii
ComponentsPeptide methionine sulfoxide reductase MsrA
KeywordsOXIDOREDUCTASE / MsrA / Clostridium oremlandii / truncated form
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
GLYCINE / Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesAlkaliphilus oremlandii OhILAs (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7568 Å
AuthorsLee, E.H. / Hwang, K.Y. / Kim, H.-Y.
CitationJournal: Plos One / Year: 2015
Title: Essential role of the C-terminal helical domain in active site formation of selenoprotein MsrA from Clostridium oremlandii
Authors: Lee, E.H. / Lee, K. / Hwang, K.Y. / Kim, H.-Y.
History
DepositionAug 23, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_initial_refinement_model / pdbx_prerelease_seq / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)33,1574
Polymers33,0072
Non-polymers1502
Water2,072115
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-4 kcal/mol
Surface area19080 Å2
Unit cell
Length a, b, c (Å)65.851, 94.475, 122.647
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11B-353-

HOH

21B-355-

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: 16503.271 Da / Num. of mol.: 2 / Fragment: UNP residues 1-144 / Mutation: U16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii OhILAs (bacteria)
Gene: msrA, Clos_1947 / Plasmid: pET21b / Production host: Escherichia coli (E. coli)
References: UniProt: A8MI53, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-GLY / GLYCINE / Glycine


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H5NO2
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 3.04 Å3/Da / Density % sol: 59.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris-HCl, 3.2 M NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 36941 / % possible obs: 96.4 % / Redundancy: 8.9 % / Biso Wilson estimate: 26.65 Å2 / Net I/σ(I): 49.7

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.8.1_1168)refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWJ

4lwj


Resolution: 1.7568→32.6 Å / FOM work R set: 0.7456 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 0.11 / Phase error: 31.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2752 1997 5.41 %Random selection
Rwork0.2262 34944 --
obs0.2288 36941 96.12 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 84.77 Å2 / Biso mean: 33.92 Å2 / Biso min: 11.13 Å2
Refinement stepCycle: final / Resolution: 1.7568→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 10 115 2312
Biso mean--48.07 30.09 -
Num. residues----271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162256
X-RAY DIFFRACTIONf_angle_d1.6133061
X-RAY DIFFRACTIONf_chiral_restr0.12317
X-RAY DIFFRACTIONf_plane_restr0.007399
X-RAY DIFFRACTIONf_dihedral_angle_d16.106803
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.758-1.8020.41561350.40172369250492
1.802-1.85070.43191400.37172443258396
1.8507-1.90520.38461410.33172466260797
1.9052-1.96670.3411420.29652505264798
1.9667-2.03690.30461440.25492501264598
2.0369-2.11850.30621460.22572546269298
2.1185-2.21490.27191450.19892555270099
2.2149-2.33160.26571440.20022519266399
2.3316-2.47770.28631470.21082567271499
2.4777-2.66890.25451470.21932571271899
2.6689-2.93730.24381480.221325882736100
2.9373-3.3620.27051490.20642599274899
3.362-4.23430.24141360.20512377251390
4.2343-32.60540.26331330.21552338247185

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