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- PDB-3pin: Crystal structure of Mxr1 from Saccharomyces cerevisiae in comple... -

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Basic information

Entry
Database: PDB / ID: 3pin
TitleCrystal structure of Mxr1 from Saccharomyces cerevisiae in complex with Trx2
Components
  • Peptide methionine sulfoxide reductase
  • Thioredoxin-2
KeywordsELECTRON TRANSPORT/Oxidoreductase / methionine-S-sulfoxide reductase / thioredoxin / ELECTRON TRANSPORT-Oxidoreductase complex
Function / homology
Function and homology information


membrane fusion priming complex / TP53 Regulates Metabolic Genes / : / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / vacuole inheritance / vacuole fusion, non-autophagic / sulfate assimilation ...membrane fusion priming complex / TP53 Regulates Metabolic Genes / : / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / Interconversion of nucleotide di- and triphosphates / The NLRP3 inflammasome / vacuole inheritance / vacuole fusion, non-autophagic / sulfate assimilation / Detoxification of Reactive Oxygen Species / disulfide oxidoreductase activity / fungal-type vacuole / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / Oxidative Stress Induced Senescence / deoxyribonucleotide biosynthetic process / protein-disulfide reductase activity / endoplasmic reticulum to Golgi vesicle-mediated transport / glutathione metabolic process / cell redox homeostasis / protein transport / cellular response to oxidative stress / Golgi membrane / nucleus / cytoplasm / cytosol
Similarity search - Function
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 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. ...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 / Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thioredoxin-2 / Peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsMa, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Structural plasticity of the thioredoxin recognition site of yeast methionine S-sulfoxide reductase Mxr1
Authors: Ma, X.X. / Guo, P.C. / Shi, W.W. / Luo, M. / Tan, X.F. / Chen, Y. / Zhou, C.Z.
History
DepositionNov 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 9, 2014Group: Database references
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thioredoxin-2
B: Peptide methionine sulfoxide reductase


Theoretical massNumber of molelcules
Total (without water)32,1732
Polymers32,1732
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-9 kcal/mol
Surface area12560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.266, 122.266, 122.266
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein Thioredoxin-2 / Thioredoxin II / TR-II / Thioredoxin-1


Mass: 11197.771 Da / Num. of mol.: 1 / Mutation: C34S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: TRX2 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / References: UniProt: P22803
#2: Protein Peptide methionine sulfoxide reductase / Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase / Protein-methionine-S-oxide reductase


Mass: 20975.432 Da / Num. of mol.: 1 / Mutation: C23S, C25S, C44S, C68S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MXR1 / Plasmid: pET29b / Production host: Escherichia coli (E. coli)
References: UniProt: P40029, peptide-methionine (S)-S-oxide reductase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.37 Å3/Da / Density % sol: 48.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 8.5
Details: 0.2M trimethylamine N-oxide, 0.1M Tris, 20% polyethylene glycol 2000 monomethyl ether, pH 8.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8320 / % possible obs: 98 %
Reflection shellResolution: 2.7→2.8 Å / % possible all: 98.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.5.0072refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PIL, 2FA4

3pil

2fa4


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.902 / SU B: 39.132 / SU ML: 0.353 / Cross valid method: THROUGHOUT / ESU R Free: 0.381 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27882 393 4.7 %RANDOM
Rwork0.23443 ---
obs0.23661 7926 97.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 62.271 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 0 15 1939
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221966
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9881.9562657
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1185238
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.83624.71387
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.26115341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.86157
X-RAY DIFFRACTIONr_chiral_restr0.0750.2293
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211467
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_it0.1781.51209
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.35421946
X-RAY DIFFRACTIONr_scbond_it0.5383757
X-RAY DIFFRACTIONr_scangle_it0.9654.5711
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.703→2.773 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 36 -
Rwork0.342 588 -
obs--98.58 %
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)
16.7541-1.37670.23515.21410.54656.0003-0.04120.71330.1816-0.6373-0.0030.3798-0.3697-0.22290.04420.24630.0499-0.01010.32260.07270.121-0.975-46.30915.746
26.25690.01280.07085.58110.83623.33650.1148-0.5391-0.1960.50090.0921-0.0157-0.03240.0794-0.20690.24920.0168-0.01260.27150.01070.047222.144-58.17632.034
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 104
2X-RAY DIFFRACTION2B3 - 183

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