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- PDB-3pil: Crystal structure of Mxr1 from Saccharomyces cerevisiae in reduce... -

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Basic information

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


: / 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
ACETATE ION / Peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.04 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 ...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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase
B: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3124
Polymers42,1932
Non-polymers1182
Water6,161342
1
A: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1562
Polymers21,0971
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1562
Polymers21,0971
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.310, 70.140, 74.030
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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: 21096.746 Da / Num. of mol.: 2
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: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 342 / 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: 1.98 Å3/Da / Density % sol: 37.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 4.6
Details: 0.2M ammonium acetate, 0.1M sodium acetate, 30% polyethylene glycol 4,000, pH 4.6, VAPOR DIFFUSION, temperature 289K

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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: Dec 26, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.03→29.17 Å / Num. obs: 21889 / % possible obs: 98.4 %
Reflection shellResolution: 2.03→2.14 Å / % possible all: 89.6

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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
Starting model: 3BQE

3bqe


Resolution: 2.04→29.17 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.913 / SU B: 10.98 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24665 1117 5.1 %RANDOM
Rwork0.2066 ---
obs0.20858 20726 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.236 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2--0.79 Å20 Å2
3----0.66 Å2
Refinement stepCycle: LAST / Resolution: 2.04→29.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2942 0 8 342 3292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223024
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8281.9564087
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.4035362
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.76624.384146
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.71615525
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3931514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2425
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0212320
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_it0.111.51819
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.21422933
X-RAY DIFFRACTIONr_scbond_it0.2831205
X-RAY DIFFRACTIONr_scangle_it0.4954.51154
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.04→2.093 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 73 -
Rwork0.265 1438 -
obs--96.61 %
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)
10.37380.136-0.03430.30430.01230.34380.0023-0.0052-0.00690.009-0.01010.00280.01150.0090.00790.000600.00030.00060.00010.00040.899710.0741-16.8145
20.3354-0.07090.06620.3189-0.00840.3134-0.0210.0028-0.00060.00620.01530.0204-0.00740.02080.00570.0014-0.00030.00010.00220.00140.00151.70621.258716.9931
345.357827.934119.166117.203711.80368.0988-0.10870.11020.055-0.07020.07740.0321-0.04920.04490.03130.01940.0155-0.00140.0417-0.02580.02193.793113.62967.2497
41.86650.033311.77170.00060.209774.2408-0.0167-0.01660.0023-0.00030.00150.0003-0.1172-0.10520.01520.002-0.00270.00570.0112-0.00040.03041.842317.3483-6.3595
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 183
2X-RAY DIFFRACTION2B3 - 183
3X-RAY DIFFRACTION3B185
4X-RAY DIFFRACTION4A185

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