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- PDB-3ksh: Structure of fRMsr of Staphylococcus aureus (oxidized form) -

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Basic information

Entry
Database: PDB / ID: 3ksh
TitleStructure of fRMsr of Staphylococcus aureus (oxidized form)
ComponentsPutative uncharacterized protein
KeywordsOXIDOREDUCTASE / fRMsr / free-Met-R-SO
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase activity / cytosol
Similarity search - Function
Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / : / GAF domain / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase ...Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / : / GAF domain / GAF domain / GAF domain / Domain present in phytochromes and cGMP-specific phosphodiesterases. / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
GAF domain-containing protein / GAF domain-containing protein
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBong, S.M. / Chi, Y.M.
CitationJournal: To be Published
Title: Structure of fRMsr of Staphylococcus aureus
Authors: Bong, S.M. / Chi, Y.M.
History
DepositionNov 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 26, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 1.3Oct 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: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,1373
Polymers17,9441
Non-polymers1922
Water2,126118
1
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,2736
Polymers35,8892
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_554x-y,-y,-z-11
Buried area1910 Å2
ΔGint-7 kcal/mol
Surface area13910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.993, 89.993, 88.538
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Putative uncharacterized protein / Free-methionine (R)-S-oxide reductase / free-R-methionine sulfoxide reductase


Mass: 17944.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: MRSA252 / Gene: SAR1796 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q6GFY9, UniProt: A0A7U7EVB7*PLUS, L-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 118 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 2M ammonium sulfate, 7% 2-propanol, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.2386 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 31, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2386 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 33964 / % possible obs: 87.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
CNS1.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHM

1vhm


Resolution: 1.5→40.11 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.259 3385 random
Rwork0.245 --
all0.292 33928 -
obs0.292 30548 -
Solvent computationBsol: 46.991 Å2
Displacement parametersBiso mean: 22.77 Å2
Baniso -1Baniso -2Baniso -3
1-1.459 Å20 Å20 Å2
2--1.459 Å20 Å2
3----2.918 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.2 Å0.18 Å
Refinement stepCycle: LAST / Resolution: 1.5→40.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1186 0 10 118 1314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_d0.004
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d23
X-RAY DIFFRACTIONc_improper_angle_d0.72
LS refinement shellResolution: 1.5→1.59 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.326 508 -
Rwork0.304 --
obs-4645 92.1 %

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