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- PDB-5g1k: A triple mutant of DsbG engineered for denitrosylation -

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Basic information

Entry
Database: PDB / ID: 5g1k
TitleA triple mutant of DsbG engineered for denitrosylation
ComponentsTHIOL DISULFIDE INTERCHANGE PROTEIN DSBG
KeywordsISOMERASE / S-(DE)NITROSYLATION / TRX FAMILY / CXXC MOTIF / DSBG
Function / homology
Function and homology information


protein disulfide isomerase activity / chaperone-mediated protein folding / outer membrane-bounded periplasmic space / protein homodimerization activity
Similarity search - Function
Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulphide bond isomerase DsbC/G, N-terminal domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Nuclear Transport Factor 2; Chain: A, / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbG
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsTamu Dufe, V. / Van Molle, I. / Lafaye, C. / Wahni, K. / Boudier, A. / Leroy, P. / Collet, J.F. / Messens, J.
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Sulfur Denitrosylation by an Engineered Trx-Like Dsbg Enzyme Identifies Nucleophilic Cysteine Hydrogen Bonds as Key Functional Determinant.
Authors: Lafaye, C. / Van Molle, I. / Tamu Dufe, V. / Wahni, K. / Boudier, A. / Leroy, P. / Collet, J. / Messens, J.
History
DepositionMar 28, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 25, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 8, 2016Group: Database references / Derived calculations
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 10, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
B: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,3605
Polymers57,0722
Non-polymers2883
Water5,639313
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-6.8 kcal/mol
Surface area25650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.920, 57.220, 86.040
Angle α, β, γ (deg.)90.00, 94.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein THIOL DISULFIDE INTERCHANGE PROTEIN DSBG


Mass: 28536.098 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P77202
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 313 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP110G, Y111P AND T200M MUTATIONS

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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: 2.6 Å3/Da / Density % sol: 52.7 % / Description: NONE
Crystal growDetails: 0.1 M SODIUM CITRATE PH 3.75, 0.2 M AMMONIUM SULFATE, 20% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012 / Details: KIRKPATRICK-BAEZ PAIR OF BI-MORPH MIRRORS
RadiationMonochromator: CHANNEL CUT CRYOGENICALLY COOLED MONOCHROMATOR CRYSTAL
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 1.96→46.44 Å / Num. obs: 40638 / % possible obs: 99.4 % / Observed criterion σ(I): 3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.73 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.58
Reflection shellResolution: 1.96→2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 3.53 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V57

1v57


Resolution: 1.96→42.872 Å / SU ML: 0.23 / σ(F): 2 / Phase error: 23.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2408 4063 10 %
Rwork0.1916 --
obs0.1965 40638 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.4 Å2
Refinement stepCycle: LAST / Resolution: 1.96→42.872 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3455 0 15 313 3783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073662
X-RAY DIFFRACTIONf_angle_d0.95018
X-RAY DIFFRACTIONf_dihedral_angle_d14.6932222
X-RAY DIFFRACTIONf_chiral_restr0.06554
X-RAY DIFFRACTIONf_plane_restr0.008655
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.96-1.98310.25911360.21461218X-RAY DIFFRACTION100
1.9831-2.00720.27261390.21611250X-RAY DIFFRACTION100
2.0072-2.03270.30091440.21921297X-RAY DIFFRACTION100
2.0327-2.05940.26671380.20961247X-RAY DIFFRACTION100
2.0594-2.08760.26841380.21221241X-RAY DIFFRACTION100
2.0876-2.11740.27651430.19861288X-RAY DIFFRACTION100
2.1174-2.1490.281380.19771242X-RAY DIFFRACTION100
2.149-2.18260.24821400.19991256X-RAY DIFFRACTION100
2.1826-2.21840.24931390.18831257X-RAY DIFFRACTION100
2.2184-2.25670.23961410.18851264X-RAY DIFFRACTION99
2.2567-2.29770.25941410.19461269X-RAY DIFFRACTION100
2.2977-2.34190.24461390.19481249X-RAY DIFFRACTION100
2.3419-2.38970.26771400.20571267X-RAY DIFFRACTION100
2.3897-2.44160.2761370.19911232X-RAY DIFFRACTION99
2.4416-2.49840.25361430.19611285X-RAY DIFFRACTION100
2.4984-2.56090.28481390.2161253X-RAY DIFFRACTION100
2.5609-2.63010.27331390.20971250X-RAY DIFFRACTION100
2.6301-2.70750.261430.21081285X-RAY DIFFRACTION99
2.7075-2.79490.26841390.20771254X-RAY DIFFRACTION100
2.7949-2.89480.25561390.20411253X-RAY DIFFRACTION99
2.8948-3.01060.24061410.20171267X-RAY DIFFRACTION99
3.0106-3.14760.27781410.19541265X-RAY DIFFRACTION99
3.1476-3.31350.25691380.19871244X-RAY DIFFRACTION99
3.3135-3.5210.2211400.17551256X-RAY DIFFRACTION99
3.521-3.79270.20881410.17941271X-RAY DIFFRACTION98
3.7927-4.17410.20381400.16381264X-RAY DIFFRACTION98
4.1741-4.77740.22761400.17271261X-RAY DIFFRACTION99
4.7774-6.01640.21671420.18711284X-RAY DIFFRACTION99
6.0164-42.88240.19691450.19011306X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 57.7015 Å / Origin y: 35.801 Å / Origin z: 19.0719 Å
111213212223313233
T0.2324 Å2-0.0146 Å20.0058 Å2-0.2241 Å2-0.0001 Å2--0.2162 Å2
L0.4227 °20.3037 °20.1346 °2-0.2126 °20.0972 °2---0.1485 °2
S0.0131 Å °0.0678 Å °0.0431 Å °0.0248 Å °0.0063 Å °0.018 Å °-0.0057 Å °0.0316 Å °-0.0194 Å °
Refinement TLS groupSelection details: ALL

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