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- PDB-7c13: beta1 domain-swapped structure of monothiol cGrx1(C16S) -

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Basic information

Entry
Database: PDB / ID: 7c13
Titlebeta1 domain-swapped structure of monothiol cGrx1(C16S)
Components
  • Glutaredoxin
  • Peptide methionine sulfoxide reductase MsrA
KeywordsOXIDOREDUCTASE / glutaredoxin-1 / Grx1 / domain-swapping
Function / homology
Function and homology information


L-methionine (S)-S-oxide reductase activity / peptide-methionine (S)-S-oxide reductase / peptide-methionine (S)-S-oxide reductase activity / cell redox homeostasis / protein modification process / electron transfer activity
Similarity search - Function
: / Selenoprotein methionine sulfoxide reductase A, helical domain / : / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin ...: / Selenoprotein methionine sulfoxide reductase A, helical domain / : / Peptide methionine sulphoxide reductase MsrA domain / Peptide methionine sulphoxide reductase MsrA superfamily / Peptide methionine sulfoxide reductase / Glutaredoxin / Glutaredoxin / Glutaredoxin domain profile. / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Peptide methionine sulfoxide reductase MsrA / Glutaredoxin
Similarity search - Component
Biological speciesAlkaliphilus oremlandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.799 Å
AuthorsLee, K. / Hwang, K.Y.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1A44A1022589 Korea, Republic Of
National Research Foundation (NRF, Korea)2020R1A2C2005670 Korea, Republic Of
CitationJournal: Iucrj / Year: 2020
Title: Monothiol and dithiol glutaredoxin-1 from clostridium oremlandii: identification of domain-swapped structures by NMR, X-ray crystallography and HDX mass spectrometry.
Authors: Lee, K. / Yeo, K.J. / Choi, S.H. / Lee, E.H. / Kim, B.K. / Kim, S. / Cheong, H.-K. / Lee, W.-K. / Kim, H.-Y. / Hwang, E. / Woo, J.R. / Lee, S.-J. / Hwang, K.Y.
History
DepositionMay 2, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 1.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Peptide methionine sulfoxide reductase MsrA
B: Glutaredoxin
C: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)42,9403
Polymers42,9403
Non-polymers00
Water00
1
A: Peptide methionine sulfoxide reductase MsrA
B: Glutaredoxin
C: Glutaredoxin

A: Peptide methionine sulfoxide reductase MsrA
B: Glutaredoxin
C: Glutaredoxin


Theoretical massNumber of molelcules
Total (without water)85,8816
Polymers85,8816
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area10270 Å2
ΔGint-60 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)153.424, 153.424, 67.898
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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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) reductase


Mass: 23600.420 Da / Num. of mol.: 1 / Mutation: U16C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii (strain OhILAs) (bacteria)
Strain: OhILAs / Gene: msrA, Clos_1947 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A8MI53, peptide-methionine (S)-S-oxide reductase
#2: Protein Glutaredoxin


Mass: 9669.997 Da / Num. of mol.: 2 / Mutation: U13C, C16S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Alkaliphilus oremlandii (strain OhILAs) (bacteria)
Strain: OhILAs / Gene: Clos_2129 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A8MIN3
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: 5.37 Å3/Da / Density % sol: 77.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1M Sodium phosphate/Citric acid pH4.2, 0.4M Potassium phosphate (dibasic)/1.6M Sodium phosphate(monobasic)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 9, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.799→30 Å / Num. obs: 22865 / % possible obs: 99.8 % / Redundancy: 7.8 % / Rmerge(I) obs: 0.153 / Χ2: 1.467 / Net I/σ(I): 6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.8-2.855.40.44611200.962199.3
2.85-2.95.50.45211110.983199.5
2.9-2.965.60.4411401.016199.7
2.96-3.025.90.413113111100
3.02-3.0860.41211281.104199.7
3.08-3.156.30.39711351.146199.6
3.15-3.236.40.36411301.176199.8
3.23-3.326.90.33211361.173199.6
3.32-3.427.20.2911421.284199.8
3.42-3.537.80.24211151.381199.6
3.53-3.6580.21311501.437199.9
3.65-3.88.50.18511471.491199.9
3.8-3.978.70.16911291.597199.7
3.97-4.1890.14511371.692199.7
4.18-4.449.40.12511531.705199.9
4.44-4.789.60.10611531.7511100
4.78-5.269.50.10311611.602199.9
5.26-6.029.20.11311551.505199.9
6.02-7.569.60.09811691.596199.7
7.56-3010.20.06912232.197199.9

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LWJ, 7C10

4lwj

7c10


Resolution: 2.799→29.838 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 0.13 / Phase error: 23.62
RfactorNum. reflection% reflection
Rfree0.2454 2012 8.8 %
Rwork0.2117 --
obs0.2147 22857 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 157.95 Å2 / Biso mean: 45.4521 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: final / Resolution: 2.799→29.838 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2746 0 0 0 2746
Num. residues----344
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.7993-2.86920.35321430.3155142799
2.8692-2.94670.33981440.31411514100
2.9467-3.03330.34461350.30721441100
3.0333-3.13120.31461420.29631480100
3.1312-3.24290.33221500.26721503100
3.2429-3.37260.27591380.23631451100
3.3726-3.52590.24631360.2031484100
3.5259-3.71140.23781440.18831485100
3.7114-3.94350.2231450.17971484100
3.9435-4.24720.20121430.1621500100
4.2472-4.67310.20011450.15271491100
4.6731-5.3460.16021440.16161504100
5.346-6.72260.22971450.2021520100
6.7226-29.8380.22561580.20131561100
Refinement TLS params.Method: refined / Origin x: 58.0433 Å / Origin y: -53.5358 Å / Origin z: 25.6022 Å
111213212223313233
T0.2255 Å2-0.0908 Å20.0311 Å2-0.3676 Å2-0.0637 Å2--0.2054 Å2
L1.8928 °21.0528 °20.3243 °2-1.6985 °20.2129 °2--0.8798 °2
S-0.0895 Å °0.1296 Å °-0.0685 Å °-0.079 Å °-0.0054 Å °0.3438 Å °0.1115 Å °-0.3688 Å °0.0732 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA7 - 208
2X-RAY DIFFRACTION1allB4 - 74
3X-RAY DIFFRACTION1allC4 - 74

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