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- PDB-6sym: Crystal structure of Escherichia coli MsrB (reduced form) -

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Basic information

Entry
Database: PDB / ID: 6sym
TitleCrystal structure of Escherichia coli MsrB (reduced form)
ComponentsPeptide methionine sulfoxide reductase MsrB
KeywordsOXIDOREDUCTASE / Reductase / Zinc-binding / R-Methionine sulfoxide reductase / Oxidative stress
Function / homology
Function and homology information


L-methionine (R)-S-oxide reductase activity / peptide-methionine (R)-S-oxide reductase / peptide-methionine (R)-S-oxide reductase activity / protein repair / response to cadmium ion / response to oxidative stress / iron ion binding / zinc ion binding / cytoplasm / cytosol
Similarity search - Function
Peptide methionine sulfoxide reductase MsrB / Peptide methionine sulphoxide reductase MrsB domain / SelR domain / Methionine-R-sulfoxide reductase (MsrB) domain profile. / Mss4-like superfamily
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrB
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6302 Å
AuthorsNapolitano, S. / Zyla, D. / Glockshuber, R.
CitationJournal: To Be Published
Title: Structure of Peptide methionine sulfoxide reductase MsrB at 1.63 Angstrom resolution
Authors: Napolitano, S. / Zyla, D. / Glockshuber, R.
History
DepositionSep 30, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)31,3134
Polymers31,1822
Non-polymers1312
Water3,153175
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A: Peptide methionine sulfoxide reductase MsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6572
Polymers15,5911
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptide methionine sulfoxide reductase MsrB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6572
Polymers15,5911
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.390, 56.270, 85.610
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptide methionine sulfoxide reductase MsrB / Peptide-methionine (R)-S-oxide reductase


Mass: 15591.161 Da / Num. of mol.: 2 / Mutation: CYS118CAF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: msrB, yeaA, b1778, JW1767 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A746, peptide-methionine (R)-S-oxide reductase
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.08 Å3/Da / Density % sol: 40.81 % / Description: Small rectangular shape.
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 0.1M sodium cacodylate pH 6, 30% PEG 2K MME, 0.2M MgCl2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.28 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Nov 25, 2018
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28 Å / Relative weight: 1
ReflectionResolution: 1.63→50 Å / Num. obs: 61381 / % possible obs: 98.7 % / Redundancy: 6.776 % / Biso Wilson estimate: 34.726 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.139 / Rrim(I) all: 0.15 / Χ2: 1.15 / Net I/σ(I): 8.47
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.63-1.671.6771.2150.6941400.3051.64389.4
1.67-1.721.7070.9770.8842950.4061.31595.5
1.72-1.775.2171.1441.5343080.6081.25498.6
1.77-1.827.8691.0292.1842140.7381.10499.9
1.82-1.887.5150.8152.6741100.7860.87899.9
1.88-1.957.490.6963.0839620.850.74899.8
1.95-2.028.1080.5714.0338140.8780.61299.9
2.02-2.17.8450.4055.5236890.9460.435100
2.1-2.27.6160.3156.6935240.9580.34100
2.2-2.317.4280.2358.9133900.9730.25499.9
2.31-2.437.3450.20810.6732190.9820.22499.9
2.43-2.586.9560.19912.3730150.9730.21799.6
2.58-2.767.9820.1915.0928620.9840.20499.8
2.76-2.988.6570.17518.126690.9840.186100
2.98-3.268.5970.14319.4324080.9930.15399.8
3.26-3.658.3280.11321.0322120.9940.12199.8
3.65-4.217.9060.09322.2319400.9950.09999.8
4.21-5.167.140.07721.9816400.9960.08399.1
5.16-7.298.6070.08324.1912760.9950.089100
7.29-7.298.4410.06926.346940.9930.073100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.14-3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model obtained from Phyre2

Resolution: 1.6302→47.0417 Å / Cross valid method: THROUGHOUT /
Num. reflection% reflection
obs61381 98.7 %
Displacement parametersBiso max: 108.22 Å2 / Biso mean: 38.8396 Å2 / Biso min: 18.13 Å2
Refinement stepCycle: LAST / Resolution: 1.6302→47.0417 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2091 0 2 175 2268

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