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- PDB-5g1l: A double mutant of DsbG engineered for denitrosylation -

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Basic information

Entry
Database: PDB / ID: 5g1l
TitleA double 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: 1.7 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
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)57,3966
Polymers57,0122
Non-polymers3844
Water8,269459
1
A: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
B: THIOL DISULFIDE INTERCHANGE PROTEIN DSBG
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)114,79312
Polymers114,0244
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area11450 Å2
ΔGint-134.2 kcal/mol
Surface area38090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)116.650, 57.030, 85.550
Angle α, β, γ (deg.)90.00, 95.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2224-

HOH

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Components

#1: Protein THIOL DISULFIDE INTERCHANGE PROTEIN DSBG


Mass: 28506.004 Da / Num. of mol.: 2 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PET28A / 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.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 459 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsP110G, Y111P 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: 1.7→46.12 Å / Num. obs: 61466 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 3.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.73
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 2.75 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.8 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1V57

1v57


Resolution: 1.7→43.138 Å / SU ML: 0.18 / σ(F): 2.01 / Phase error: 18.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1922 6147 10 %
Rwork0.1681 --
obs0.1705 61466 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→43.138 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3467 0 20 459 3946
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073756
X-RAY DIFFRACTIONf_angle_d0.9565147
X-RAY DIFFRACTIONf_dihedral_angle_d10.3892287
X-RAY DIFFRACTIONf_chiral_restr0.065566
X-RAY DIFFRACTIONf_plane_restr0.008672
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.27881940.24351749X-RAY DIFFRACTION93
1.7193-1.73960.28042010.23891812X-RAY DIFFRACTION100
1.7396-1.76080.25512010.23091806X-RAY DIFFRACTION100
1.7608-1.78310.24662050.21151849X-RAY DIFFRACTION100
1.7831-1.80650.25142070.20811864X-RAY DIFFRACTION100
1.8065-1.83130.20352020.20611815X-RAY DIFFRACTION100
1.8313-1.85740.25642060.19691852X-RAY DIFFRACTION100
1.8574-1.88520.20442030.18651825X-RAY DIFFRACTION100
1.8852-1.91460.21382060.18741857X-RAY DIFFRACTION100
1.9146-1.9460.23332050.18071841X-RAY DIFFRACTION100
1.946-1.97960.20032050.17261846X-RAY DIFFRACTION100
1.9796-2.01560.20822040.17151840X-RAY DIFFRACTION100
2.0156-2.05430.20282030.17471821X-RAY DIFFRACTION100
2.0543-2.09630.21572070.18461867X-RAY DIFFRACTION100
2.0963-2.14190.20412050.17711841X-RAY DIFFRACTION100
2.1419-2.19170.18982050.16721853X-RAY DIFFRACTION100
2.1917-2.24650.17432040.15681831X-RAY DIFFRACTION100
2.2465-2.30720.18892040.16191841X-RAY DIFFRACTION100
2.3072-2.37510.19782070.16931858X-RAY DIFFRACTION100
2.3751-2.45180.21122040.16861836X-RAY DIFFRACTION100
2.4518-2.53940.20022040.1711837X-RAY DIFFRACTION100
2.5394-2.6410.20012060.1741854X-RAY DIFFRACTION100
2.641-2.76120.20552040.17521840X-RAY DIFFRACTION100
2.7612-2.90680.20522060.17511855X-RAY DIFFRACTION100
2.9068-3.08880.19882070.17931860X-RAY DIFFRACTION99
3.0888-3.32720.18882070.16981857X-RAY DIFFRACTION100
3.3272-3.66190.16572050.14921854X-RAY DIFFRACTION100
3.6619-4.19140.15162070.13821854X-RAY DIFFRACTION99
4.1914-5.27930.16732090.13851886X-RAY DIFFRACTION99
5.2793-43.15150.17472140.16961918X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 57.3098 Å / Origin y: 35.5353 Å / Origin z: 18.8667 Å
111213212223313233
T0.1678 Å2-0.0002 Å20.0072 Å2-0.1671 Å20.0009 Å2--0.1701 Å2
L0.3595 °20.2096 °20.0884 °2-0.1877 °20.062 °2--0.0213 °2
S0.0217 Å °0.0174 Å °0.0408 Å °0.0148 Å °-0.0186 Å °0.0187 Å °-0.0082 Å °-0.0008 Å °-0.0035 Å °
Refinement TLS groupSelection details: ALL

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