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- PDB-6agv: Crystal structure of apo mouse MsrA -

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Basic information

Entry
Database: PDB / ID: 6agv
TitleCrystal structure of apo mouse MsrA
ComponentsMitochondrial peptide methionine sulfoxide reductase
KeywordsOXIDOREDUCTASE / Methionine sulfoxide / MsrA
Function / homology
Function and homology information


Protein repair / L-methionine (S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / nuclear body / mitochondrion / membrane / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Mitochondrial peptide methionine sulfoxide reductase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsHwang, K.Y. / Kim, J.S.
CitationJournal: To Be Published
Title: Crystal structure of apo mouse MsrA
Authors: Hwang, K.Y. / Kim, J.S.
History
DepositionAug 14, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mitochondrial peptide methionine sulfoxide reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1152
Polymers26,0231
Non-polymers921
Water6,017334
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area230 Å2
ΔGint-1 kcal/mol
Surface area9530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.825, 52.634, 70.670
Angle α, β, γ (deg.)90.000, 118.669, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-688-

HOH

21A-728-

HOH

31A-731-

HOH

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Components

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


Mass: 26023.398 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Msra / Production host: Escherichia coli (E. coli)
References: UniProt: Q9D6Y7, peptide-methionine (S)-S-oxide reductase
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 334 / 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: 2.44 Å3/Da / Density % sol: 49.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Tris pH 9.0, 0.2M NaCl, 26% polyethylene glycol 3350, 0.1M Sodium Iodide and were used in ratio of 1:1.35 (mouse MsrA and Trx peptide)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.62→50 Å / Num. obs: 165785 / % possible obs: 96.9 % / Redundancy: 5.3 % / Biso Wilson estimate: 16.2 Å2 / Rsym value: 0.037 / Net I/σ(I): 51.72
Reflection shellResolution: 1.62→1.65 Å / Mean I/σ(I) obs: 7.03 / Rsym value: 0.178 / % possible all: 91

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Processing

Software
NameVersionClassification
PHASER1.13_2998phasing
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→30.68 Å / SU ML: 0.1355 / Cross valid method: FREE R-VALUE / σ(F): 1.52 / Phase error: 17.018
RfactorNum. reflection% reflection
Rfree0.186 1997 6.44 %
Rwork0.1608 --
obs0.1625 30995 96.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 22.46 Å2
Refinement stepCycle: LAST / Resolution: 1.62→30.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1523 0 6 334 1863
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621572
X-RAY DIFFRACTIONf_angle_d0.84012128
X-RAY DIFFRACTIONf_chiral_restr0.0572216
X-RAY DIFFRACTIONf_plane_restr0.0059280
X-RAY DIFFRACTIONf_dihedral_angle_d15.9397921
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.660.21251430.18551928X-RAY DIFFRACTION92.25
1.66-1.710.21461340.17572009X-RAY DIFFRACTION94.95
1.71-1.760.18141420.17512012X-RAY DIFFRACTION95.18
1.76-1.810.19231400.17472092X-RAY DIFFRACTION96.46
1.81-1.880.1971400.16422041X-RAY DIFFRACTION95.87
1.88-1.950.19471380.16852071X-RAY DIFFRACTION97.14
1.95-2.040.18381470.16422067X-RAY DIFFRACTION97.45
2.04-2.150.22391440.17072099X-RAY DIFFRACTION98.51
2.15-2.280.2221420.16452080X-RAY DIFFRACTION98.49
2.28-2.460.19921500.17092126X-RAY DIFFRACTION98.91
2.46-2.710.20721350.16542130X-RAY DIFFRACTION99.12
2.71-3.10.18391470.16172140X-RAY DIFFRACTION99.35
3.1-3.90.15321470.14792083X-RAY DIFFRACTION96.83
3.9-30.690.16361480.14682120X-RAY DIFFRACTION96.14

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