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- PDB-6yev: Crystal structure of MsrA C206 and Trx C35S complex from Escheric... -

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Basic information

Entry
Database: PDB / ID: 6yev
TitleCrystal structure of MsrA C206 and Trx C35S complex from Escherichia coli
Components
  • Peptide methionine sulfoxide reductase MsrA
  • Thioredoxin 1
KeywordsOXIDOREDUCTASE / Reductase / S-Methionine sulfoxide reductase / Oxidative stress / complex / thioredoxin
Function / homology
Function and homology information


L-methionine-(S)-S-oxide reductase activity / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / protein modification process / cellular response to oxidative stress ...L-methionine-(S)-S-oxide reductase activity / oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein repair / DNA polymerase processivity factor activity / protein-disulfide reductase activity / cell redox homeostasis / protein modification process / cellular response to oxidative stress / response to oxidative stress / cytoplasm / cytosol
Similarity search - Function
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 / Thioredoxin-like superfamily
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrA / Thioredoxin 1
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.94 Å
AuthorsNapolitano, S. / Zyla, D. / Glockshuber, R.
CitationJournal: To Be Published
Title: Structure of a complex between the single-cysteine mutant MsrA C206 and Trx C35S from Escherichia coli
Authors: Napolitano, S. / Zyla, D. / Glockshuber, R.
History
DepositionMar 25, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: Thioredoxin 1
F: Thioredoxin 1
A: Peptide methionine sulfoxide reductase MsrA
B: Peptide methionine sulfoxide reductase MsrA
C: Peptide methionine sulfoxide reductase MsrA
D: Peptide methionine sulfoxide reductase MsrA
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,45911
Polymers128,3677
Non-polymers924
Water61334
1
E: Thioredoxin 1
A: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0653
Polymers35,0422
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-20 kcal/mol
Surface area14740 Å2
MethodPISA
2
F: Thioredoxin 1
B: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0653
Polymers35,0422
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-20 kcal/mol
Surface area14680 Å2
MethodPISA
3
C: Peptide methionine sulfoxide reductase MsrA
G: Thioredoxin 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0653
Polymers35,0422
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1210 Å2
ΔGint-21 kcal/mol
Surface area15000 Å2
MethodPISA
4
D: Peptide methionine sulfoxide reductase MsrA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2632
Polymers23,2401
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area170 Å2
ΔGint-11 kcal/mol
Surface area9550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.910, 139.910, 218.050
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11C-402-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and ((resid 7 and (name N or name...
21(chain B and ((resid 7 and (name N or name...
31(chain C and ((resid 7 and (name N or name...
41(chain D and ((resid 7 and (name N or name...
12(chain E and (resid 4 through 51 or resid 53...
22(chain F and (resid 4 through 51 or resid 53...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and ((resid 7 and (name N or name...A7
121(chain A and ((resid 7 and (name N or name...A3 - 211
131(chain A and ((resid 7 and (name N or name...A3 - 211
141(chain A and ((resid 7 and (name N or name...A3 - 211
151(chain A and ((resid 7 and (name N or name...A3 - 211
211(chain B and ((resid 7 and (name N or name...B7
221(chain B and ((resid 7 and (name N or name...B4 - 210
231(chain B and ((resid 7 and (name N or name...B4 - 210
241(chain B and ((resid 7 and (name N or name...B4 - 210
251(chain B and ((resid 7 and (name N or name...B4 - 210
311(chain C and ((resid 7 and (name N or name...C7
321(chain C and ((resid 7 and (name N or name...C3 - 210
331(chain C and ((resid 7 and (name N or name...C3 - 210
341(chain C and ((resid 7 and (name N or name...C3 - 210
351(chain C and ((resid 7 and (name N or name...C3 - 210
411(chain D and ((resid 7 and (name N or name...D7
421(chain D and ((resid 7 and (name N or name...D6 - 206
431(chain D and ((resid 7 and (name N or name...D6 - 206
441(chain D and ((resid 7 and (name N or name...D6 - 206
451(chain D and ((resid 7 and (name N or name...D6 - 206
112(chain E and (resid 4 through 51 or resid 53...E4 - 51
122(chain E and (resid 4 through 51 or resid 53...E53 - 72
132(chain E and (resid 4 through 51 or resid 53...E74 - 84
142(chain E and (resid 4 through 51 or resid 53...E86 - 95
152(chain E and (resid 4 through 51 or resid 53...E97 - 99
212(chain F and (resid 4 through 51 or resid 53...F4 - 51
222(chain F and (resid 4 through 51 or resid 53...F53 - 72
232(chain F and (resid 4 through 51 or resid 53...F1 - 108
242(chain F and (resid 4 through 51 or resid 53...F0
252(chain F and (resid 4 through 51 or resid 53...F97 - 99

NCS ensembles :
ID
1
2

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Components

#1: Protein Thioredoxin 1 / Trx-1


Mass: 11802.517 Da / Num. of mol.: 3 / Mutation: Cys35Ser
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: trxA, fipA, tsnC, b3781, JW5856 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P0AA25
#2: Protein
Peptide methionine sulfoxide reductase MsrA / Protein-methionine-S-oxide reductase / Peptide-methionine (S)-S-oxide reductase / Peptide Met(O) reductase


Mass: 23239.787 Da / Num. of mol.: 4 / Mutation: Cys51Ala, Cys86Ala, Cys198Ala
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: msrA, pms, b4219, JW4178 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P0A744, peptide-methionine (S)-S-oxide reductase
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 34 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 4.8 Å3/Da / Density % sol: 74.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M BIS-TRIS propane pH 6.5, 0.2M trisodium citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.94→49.71 Å / Num. obs: 53069 / % possible obs: 99.85 % / Redundancy: 39.8 % / Rrim(I) all: 0.55 / Net I/σ(I): 0.47
Reflection shellResolution: 2.94→3.01 Å / Num. unique obs: 5325 / CC1/2: 0.112

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17rc5_3630refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2trx, 1ff3

2trx

1ff3


Resolution: 2.94→49.71 Å / SU ML: 0.48 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.88
RfactorNum. reflection% reflection
Rfree0.2576 2653 5 %
Rwork0.2288 --
obs0.2302 53069 99.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 242.59 Å2 / Biso mean: 97.0643 Å2 / Biso min: 41.82 Å2
Refinement stepCycle: final / Resolution: 2.94→49.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8773 0 4 34 8811
Biso mean--79.24 58.89 -
Num. residues----1142
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2284X-RAY DIFFRACTION6.827TORSIONAL
12B2284X-RAY DIFFRACTION6.827TORSIONAL
13C2284X-RAY DIFFRACTION6.827TORSIONAL
14D2284X-RAY DIFFRACTION6.827TORSIONAL
21E522X-RAY DIFFRACTION6.827TORSIONAL
22F522X-RAY DIFFRACTION6.827TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.94-2.990.38931360.346125992735100
2.99-3.050.36191390.351726422781100
3.05-3.110.37471390.330126262765100
3.11-3.180.36751370.325326002737100
3.18-3.250.31941390.311826472786100
3.26-3.340.35721370.312926102747100
3.34-3.430.35681380.296326182756100
3.43-3.530.32261390.277626422781100
3.53-3.640.28551390.245426412780100
3.64-3.770.26311390.224926362775100
3.77-3.920.23721390.22126372776100
3.92-4.10.26851380.224826472785100
4.1-4.320.24741400.225226542794100
4.32-4.590.24581390.204626522791100
4.59-4.940.21821400.18926822822100
4.94-5.440.21711400.182226652805100
5.44-6.220.22621420.193626932835100
6.22-7.830.20381430.204727172860100
7.84-49.710.24291500.22012808295899
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)
11.1672-0.44570.50862.1437-0.03971.5086-0.27920.71630.262-1.23980.07580.6597-0.6055-0.3751-0.00051.09930.0714-0.26140.97170.10651.034638.6421-22.4305-9.2713
21.69970.17240.03131.67880.23872.24630.2157-0.5398-0.06020.13090.1050.4067-0.3405-0.8126-0.00070.73350.01190.01891.37210.21521.087740.8009-31.758862.6248
32.2331-0.47010.01242.42310.39921.12390.0588-0.1158-0.1386-0.0380.1503-0.14530.10870.0770.00010.7515-0.0632-0.1110.7777-0.00720.730564.1054-40.5382.4295
42.340.8477-0.19761.5592-0.38352.78380.1569-0.1615-0.2952-0.03520.05110.1604-0.2437-0.3373-0.00030.68880.0012-0.04150.72410.05730.734651.8542-22.311631.4715
51.6723-0.14760.58181.83250.08452.7965-0.19620.3265-0.0773-0.22080.298-0.1476-0.06690.34580.00010.79-0.13460.05790.763-0.03610.758776.347-2.782413.5415
61.3162-0.35580.35791.699-1.01012.31230.1357-0.2577-0.1386-0.1714-0.1461-0.55930.16070.8831-0.00030.7286-0.0303-0.02881.2709-0.15751.082796.3526-32.973715.5934
70.00980.1066-0.11560.7483-0.81430.87680.66591.47280.3187-1.6426-0.0908-0.5119-0.33330.21130.00611.7529-0.05750.46021.388-0.09021.027892.0904-5.5316-16.4977
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'E' and resid 1 through 102)E1 - 102
2X-RAY DIFFRACTION2(chain 'F' and resid 1 through 108)F1 - 108
3X-RAY DIFFRACTION3(chain 'A' and resid 3 through 211)A3 - 211
4X-RAY DIFFRACTION4(chain 'B' and resid 4 through 210)B4 - 210
5X-RAY DIFFRACTION5(chain 'C' and resid 3 through 210)C3 - 210
6X-RAY DIFFRACTION6(chain 'D' and resid 6 through 206)D6 - 206
7X-RAY DIFFRACTION7(chain 'G' and resid 3 through 108)G3 - 108

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