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- PDB-4d7l: Methionine sulfoxide reductase A of Corynebacterium diphtheriae -

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Basic information

Entry
Database: PDB / ID: 4d7l
TitleMethionine sulfoxide reductase A of Corynebacterium diphtheriae
ComponentsPEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
KeywordsOXIDOREDUCTASE / THIOL DISULFIDE EXCHANGE
Function / homology
Function and homology information


: / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / protein modification process / cellular response to oxidative stress / 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
CACODYLATE ION / TRIETHYLENE GLYCOL / Peptide methionine sulfoxide reductase MsrA
Similarity search - Component
Biological speciesCORYNEBACTERIUM DIPHTHERIAE NCTC 13129 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.895 Å
AuthorsVan Molle, I. / Tossounian, M.A. / Pedre, B. / Wahni, K. / Vertommen, D. / Messens, J.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Corynebacterium Diphtheriae Methionine Sulfoxide Reductase a Exploits a Unique Mycothiol Redox Relay Mechanism.
Authors: Tossounian, M. / Pedre, B. / Wahni, K. / Erdogan, H. / Vertommen, D. / Van Molle, I. / Messens, J.
History
DepositionNov 25, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 18, 2015Provider: repository / Type: Initial release
Revision 1.1May 13, 2015Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 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 MSRA
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,08429
Polymers78,4353
Non-polymers3,64926
Water11,728651
1
A: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,58011
Polymers26,1451
Non-polymers1,43410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,58011
Polymers26,1451
Non-polymers1,43410
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,9257
Polymers26,1451
Non-polymers7806
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)86.395, 140.175, 140.551
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1221-

SO4

21A-2235-

HOH

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Components

#1: Protein PEPTIDE METHIONINE SULFOXIDE REDUCTASE MSRA / PROTEIN-METHIONINE-S-OXIDE REDUCTASE / PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE / PEPTIDE MET(O) ...PROTEIN-METHIONINE-S-OXIDE REDUCTASE / PEPTIDE-METHIONINE (S)-S-OXIDE REDUCTASE / PEPTIDE MET(O) REDUCTASE / METHIONINE SULFOXIDE REDUCTASE A


Mass: 26145.139 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CORYNEBACTERIUM DIPHTHERIAE NCTC 13129 (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q6NEL2
#2: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6AsO2
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 651 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE MSRA GENE WAS CLONED IN THE PET28A VECTOR, WITH A N- TERMINAL HIS-TAG AND A THROMBIN CLEAVAGE ...THE MSRA GENE WAS CLONED IN THE PET28A VECTOR, WITH A N- TERMINAL HIS-TAG AND A THROMBIN CLEAVAGE SITE, RESULTING IN THE FOLLOWING ADDITIONAL RESIDUES AT THE N-TERMINUS MGSSHHHHHH SSGLVPRGSH

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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: 2.73 Å3/Da / Density % sol: 54.94 % / Description: NONE
Crystal growpH: 7
Details: 0.1 M NA CACODYLATE PH 7.0, 0.35 M AMMONIUM SULFATE, 16% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 18, 2014
Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS PLUS CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 1.89→50 Å / Num. obs: 67677 / % possible obs: 99.7 % / Observed criterion σ(I): 3 / Redundancy: 8.85 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.79
Reflection shellResolution: 1.89→2.01 Å / Redundancy: 8.5 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2.27 / % possible all: 98.1

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FF3

1ff3


Resolution: 1.895→41.291 Å / SU ML: 0.19 / σ(F): 1.35 / Phase error: 18.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1903 3384 5 %
Rwork0.1536 --
obs0.1555 67675 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.895→41.291 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4862 0 120 651 5633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015277
X-RAY DIFFRACTIONf_angle_d1.2297213
X-RAY DIFFRACTIONf_dihedral_angle_d12.6211913
X-RAY DIFFRACTIONf_chiral_restr0.055769
X-RAY DIFFRACTIONf_plane_restr0.007964
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8948-1.92190.30931300.2732471X-RAY DIFFRACTION92
1.9219-1.95060.27891390.22412641X-RAY DIFFRACTION100
1.9506-1.9810.25851390.20462645X-RAY DIFFRACTION100
1.981-2.01350.22121420.20252696X-RAY DIFFRACTION100
2.0135-2.04820.24111380.19622626X-RAY DIFFRACTION100
2.0482-2.08550.26871400.18432666X-RAY DIFFRACTION100
2.0855-2.12560.2371410.17872669X-RAY DIFFRACTION100
2.1256-2.1690.21041420.16692691X-RAY DIFFRACTION100
2.169-2.21610.21441380.15372633X-RAY DIFFRACTION100
2.2161-2.26770.19271420.14742689X-RAY DIFFRACTION100
2.2677-2.32440.2021390.14992646X-RAY DIFFRACTION100
2.3244-2.38720.20641410.15022675X-RAY DIFFRACTION100
2.3872-2.45750.19471410.14832682X-RAY DIFFRACTION100
2.4575-2.53680.19351410.14472676X-RAY DIFFRACTION100
2.5368-2.62740.20671400.15542672X-RAY DIFFRACTION100
2.6274-2.73260.19961420.15882683X-RAY DIFFRACTION100
2.7326-2.85690.18871410.15172693X-RAY DIFFRACTION100
2.8569-3.00750.18421420.15462693X-RAY DIFFRACTION100
3.0075-3.19590.21961420.15952708X-RAY DIFFRACTION100
3.1959-3.44250.20521420.15692697X-RAY DIFFRACTION100
3.4425-3.78880.14531430.13472707X-RAY DIFFRACTION100
3.7888-4.33650.15831440.1282732X-RAY DIFFRACTION100
4.3365-5.46150.14821440.13032744X-RAY DIFFRACTION100
5.4615-41.30110.15691510.15112856X-RAY DIFFRACTION100
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)
10.8235-0.1095-0.13010.83580.01961.149-0.0198-0.0289-0.00210.0028-0.0074-0.02430.04230.05020.02380.15120.00940.00660.11990.0080.149940.817113.0178-15.7931
22.152-0.64640.33931.0829-0.09531.2649-0.02470.0330.0818-0.01220.0065-0.02940.00420.04240.01450.13950.0160.00430.12080.00310.137418.67621.846313.3214
31.49170.445-0.16121.1307-0.4141.34110.0007-0.0147-0.0242-0.0069-0.0199-0.00060.0533-0.05270.01790.1158-0.0116-0.01570.14210.00020.143162.93820.8518.6754
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESSEQ 7:219)
2X-RAY DIFFRACTION2(CHAIN B AND RESSEQ 8:220)
3X-RAY DIFFRACTION3(CHAIN C AND RESSEQ 7:219)

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