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- PDB-3pim: Crystal structure of Mxr1 from Saccharomyces cerevisiae in unusua... -

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Basic information

Entry
Database: PDB / ID: 3pim
TitleCrystal structure of Mxr1 from Saccharomyces cerevisiae in unusual oxidized form
ComponentsPeptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE / methionine-S-sulfoxide reductase
Function / homology
Function and homology information


L-methionine-(S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / cellular response to oxidative stress / nucleus / cytoplasm
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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase
B: Peptide methionine sulfoxide reductase
C: Peptide methionine sulfoxide reductase


Theoretical massNumber of molelcules
Total (without water)64,5343
Polymers64,5343
Non-polymers00
Water4,216234
1
A: Peptide methionine sulfoxide reductase
B: Peptide methionine sulfoxide reductase


Theoretical massNumber of molelcules
Total (without water)43,0222
Polymers43,0222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2930 Å2
ΔGint-17 kcal/mol
Surface area16800 Å2
MethodPISA
2
C: Peptide methionine sulfoxide reductase


Theoretical massNumber of molelcules
Total (without water)21,5111
Polymers21,5111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)111.894, 111.894, 108.124
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
DetailsAUTHOR DETERMINED BIOLOGICAL ASSEMBLY: UNKNOWN

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Components

#1: Protein Peptide methionine sulfoxide reductase / Mxr1 / Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase / Protein-methionine-S- ...Mxr1 / Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase / Protein-methionine-S-oxide reductase


Mass: 21511.191 Da / Num. of mol.: 3
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
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 3.03 Å3/Da / Density % sol: 59.38 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 5.6
Details: 0.5M ammonium sulfate, 0.1M sodium citrate, 1.0M lithium sulfate, pH 5.6, 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: 1.9→50 Å / Num. obs: 59060 / % possible obs: 95.6 %
Reflection shellResolution: 1.9→1.97 Å / % possible all: 97.8

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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

3pil


Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.9 / SU B: 6.247 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26448 2999 5.1 %RANDOM
Rwork0.2361 ---
obs0.23754 55925 95.34 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.419 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å2-0.02 Å20 Å2
2---0.04 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4187 0 0 234 4421
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224298
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.21.9465809
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6565504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45924.112214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.10715737
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9941520
X-RAY DIFFRACTIONr_chiral_restr0.0880.2604
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213291
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_it0.7461.52549
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.38824107
X-RAY DIFFRACTIONr_scbond_it1.96631749
X-RAY DIFFRACTIONr_scangle_it3.3454.51702
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.901→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 239 -
Rwork0.265 4095 -
obs--96.4 %
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)
10.2329-0.10690.01660.48410.17520.488-0.01570.01980.05710.0165-0.0174-0.0141-0.0275-0.03820.0330.07010.0372-0.01190.03140.00020.040245.039836.26615.0957
20.1790.0550.05590.4393-0.03460.3679-0.01330.0082-0.0165-0.00410.0384-0.02680.03740.0196-0.02510.07560.0236-0.00480.03090.00210.038653.427312.69859.4803
34.21780.08153.45353.35011.73813.89070.0523-0.86-0.6541-0.70930.2131-0.0352-0.2479-0.7086-0.26540.2611-0.15720.12220.310.01730.346719.4993-6.80873.3372
40.1726-0.0009-0.02520.22950.05710.2025-0.00060.00090.01520.0109-0.0213-0.02040.0171-0.03980.02190.07630.0275-0.01210.03260.00060.018346.506122.752813.0633
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 184
2X-RAY DIFFRACTION2B-2 - 184
3X-RAY DIFFRACTION3C2 - 184
4X-RAY DIFFRACTION4A185 - 286
5X-RAY DIFFRACTION4B185 - 303
6X-RAY DIFFRACTION4C185 - 234

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