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- PDB-3ko6: Crystal structure of yeast free methionine-R-sulfoxide reductase ... -

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Basic information

Entry
Database: PDB / ID: 3ko6
TitleCrystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate
ComponentsUPF0067 GAF domain-containing protein YKL069W
KeywordsOXIDOREDUCTASE / Saccharomyces cerevisiae / methionine-R-sulfoxide reductase / substrate binding / catalytic mechanism / product dissociation
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase / L-methionine (R)-S-oxide reductase activity / cellular response to oxidative stress / nucleus / cytoplasm / cytosol
Similarity search - Function
Free Met sulfoxide reductase conserved site / Uncharacterized protein family UPF0067 signature. / : / GAF domain / GAF domain / GAF domain / GAF domain / GAF-like domain superfamily / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
METHIONINE SULFOXIDE / Free methionine-R-sulfoxide reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsMa, X.-X. / Guo, P.-C. / Chen, Y. / Zhou, C.-Z.
CitationJournal: To be Published
Title: Crystal structure of yeast free methionine-R-sulfoxide reductase Ykg9 in complex with the substrate
Authors: Ma, X.-X. / Guo, P.-C. / Chen, Y. / Zhou, C.-Z.
History
DepositionNov 13, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 17, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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Assembly

Deposited unit
A: UPF0067 GAF domain-containing protein YKL069W
B: UPF0067 GAF domain-containing protein YKL069W
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8374
Polymers39,5072
Non-polymers3302
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-16 kcal/mol
Surface area15120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.548, 73.548, 163.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11B-203-

HOH

21B-240-

HOH

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Components

#1: Protein UPF0067 GAF domain-containing protein YKL069W / Ykg9


Mass: 19753.252 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: S288C / Gene: YKL069W / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P36088, L-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-SME / METHIONINE SULFOXIDE


Type: L-peptide linking / Mass: 165.211 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H11NO3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.8 Å3/Da / Density % sol: 56.06 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 2.0M (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 289.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Sep 25, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 15410 / Num. obs: 15274 / % possible obs: 99.2 % / Redundancy: 6 % / Rmerge(I) obs: 0.123 / Rsym value: 0.092 / Net I/σ(I): 15.1
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.499 / Mean I/σ(I) obs: 2.2 / Num. unique all: 1421 / Rsym value: 0.412 / % possible all: 95.3

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.55→49.561 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.901 / SU B: 20.432 / SU ML: 0.201 / Cross valid method: THROUGHOUT / ESU R: 0.522 / ESU R Free: 0.293 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25408 761 5 %RANDOM
Rwork0.20825 ---
obs0.21045 14488 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.016 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.55→49.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2718 0 20 116 2854
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222794
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9453790
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6715350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25926.508126
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.92115466
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0780.2428
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022094
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6971.51748
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.28922812
X-RAY DIFFRACTIONr_scbond_it1.54731046
X-RAY DIFFRACTIONr_scangle_it2.6514.5978
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.549→2.615 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.451 61 -
Rwork0.334 984 -
obs--94.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9721-0.73770.44180.8623-0.00470.56640.0033-0.08370.018-0.01490.0196-0.0406-0.0331-0.075-0.02290.15250.0230.01170.16740.0030.003535.63613.7677.058
20.6365-0.52610.12370.8758-0.37970.68530.0471-0.02270.0324-0.0681-0.0155-0.09110.02150.0023-0.03160.15760.0080.00820.1455-0.00110.024152.8331.353-1.662
367.1987-47.354837.973870.241-47.718233.37271.4403-0.70720.2937-0.3287-0.62181.49920.44290.2248-0.81850.95360.1044-0.03190.4190.0980.160633.09216.041-3.794
470.53-3.0803-4.440236.8952-1.90560.40080.69820.3552-0.6702-0.0205-0.72330.1245-0.05240.02620.02510.17260.02230.02950.1576-0.05060.074154.985-1.479.141
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 179
2X-RAY DIFFRACTION2B4 - 179
3X-RAY DIFFRACTION3A181
4X-RAY DIFFRACTION4B181

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