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- PDB-4u66: Induced Dimer Structure of Methionine Sulfoxide Reductase U16C fr... -

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Basic information

Entry
Database: PDB / ID: 4u66
TitleInduced Dimer 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: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
Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesAlkaliphilus oremlandii OhILAs (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsHwang, K.Y. / Lee, E.H.
CitationJournal: Plos One / Year: 2015
Title: Evidence for the Dimerization-Mediated Catalysis of Methionine Sulfoxide Reductase A from Clostridium oremlandii
Authors: Lee, E.H. / Lee, K. / Kwak, G.H. / Park, Y.S. / Lee, K.J. / Hwang, K.Y. / Kim, H.Y.
History
DepositionJul 28, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 15, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: diffrn_source / entity_src_gen ...diffrn_source / entity_src_gen / pdbx_database_status / pdbx_prerelease_seq / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag ..._diffrn_source.pdbx_synchrotron_site / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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
C: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,4776
Polymers71,1893
Non-polymers2883
Water86548
1
A: Peptide methionine sulfoxide reductase MsrA
hetero molecules

A: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6514
Polymers47,4592
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554-y,-x,-z-1/21
Buried area2640 Å2
ΔGint-40 kcal/mol
Surface area18240 Å2
MethodPISA
2
B: Peptide methionine sulfoxide reductase MsrA
C: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6514
Polymers47,4592
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-40 kcal/mol
Surface area18610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)102.564, 102.564, 227.734
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

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


Mass: 23729.600 Da / Num. of mol.: 3 / 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 BL21(DE3) (bacteria)
References: UniProt: A8MI53, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 48 / 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: 4.21 Å3/Da / Density % sol: 70.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3
Details: 0.1M TRIS-HCL, 1.2M AMMONIUM SULFATE, 12%(V/V) GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-1A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 20, 2011
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→30 Å / Num. obs: 26615 / % possible obs: 94.6 % / Observed criterion σ(I): 2 / Redundancy: 2.9 % / Biso Wilson estimate: 50.47 Å2 / Net I/σ(I): 11.6
Reflection shellResolution: 2.9→2.95 Å / Rejects: 0 / % possible all: 88.6

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Processing

Software
NameVersionClassification
HKL-2000data processing
PDB_EXTRACT3.14data extraction
PHASERmodel building
PHENIX(PHENIX.REFINE: 1.8.1_1168)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB DNTRY 4LWJ

4lwj


Resolution: 2.9→29.82 Å / SU ML: 0.59 / Cross valid method: FREE R-VALUE / σ(F): 0.2 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.279 1800 6.84 %Random selection
Rwork0.248 24500 --
obs0.251 26300 94.8 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 172.73 Å2 / Biso mean: 77.93 Å2 / Biso min: 24.39 Å2
Refinement stepCycle: final / Resolution: 2.9→29.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4887 0 15 48 4950
Biso mean--99.42 54.83 -
Num. residues----611
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.97830.4411250.40261710183588
2.9783-3.06590.38681270.37431710183789
3.0659-3.16480.37951320.33961797192992
3.1648-3.27770.33641340.32141824195894
3.2777-3.40880.28081350.28151852198795
3.4088-3.56370.29981390.25151886202596
3.5637-3.75120.24861400.22881897203797
3.7512-3.98580.24241400.2121910205097
3.9858-4.29270.25521410.19411910205196
4.2927-4.72310.2271420.1971923206597
4.7231-5.40310.25141440.20491964210897
5.4031-6.7940.27121450.25092000214598
6.794-29.82690.25881560.23032117227398

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