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- PDB-3l9s: Crystal Structure of Salmonella enterica serovar Typhimurium DsbA -

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Basic information

Entry
Database: PDB / ID: 3l9s
TitleCrystal Structure of Salmonella enterica serovar Typhimurium DsbA
ComponentsThiol:disulfide interchange protein
KeywordsOXIDOREDUCTASE / thioredoxin-fold / DsbA / thiol-disulfide oxidoreductase / Disulfide bond / Redox-active center
Function / homology
Function and homology information


cellular response to antibiotic / protein disulfide isomerase activity / protein-disulfide reductase activity / cell redox homeostasis / outer membrane-bounded periplasmic space / periplasmic space
Similarity search - Function
Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein / Thiol:disulfide interchange protein DsbA
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.58 Å
AuthorsHeras, B. / Jarrott, R. / Shouldice, S.R. / Guncar, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structural and functional characterization of three DsbA paralogues from Salmonella enterica serovar typhimurium
Authors: Heras, B. / Totsika, M. / Jarrott, R. / Shouldice, S.R. / Guncar, G. / Achard, M.E.S. / Wells, T.J. / Argente, M.P. / McEwan, A.G. / Schembri, M.A.
History
DepositionJan 5, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein


Theoretical massNumber of molelcules
Total (without water)21,2151
Polymers21,2151
Non-polymers00
Water4,666259
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.377, 61.837, 42.951
Angle α, β, γ (deg.)90.00, 101.32, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Thiol:disulfide interchange protein


Mass: 21215.115 Da / Num. of mol.: 1 / Fragment: UNP residues 19-207
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SL1344 / Gene: dsbA, STM3997 / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)/plyss
References: UniProt: E1WE53, UniProt: P0A2H9*PLUS, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 46.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1M ammonium sulfate, 1% (w/v) polyethylene glycol 3350, 100mM 2,2-bis(hydroxymethyl)-2,2',2"-nitrilotriethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.956667 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2008 / Details: mirrors
RadiationMonochromator: Double Si with sagittaly bent second crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956667 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. all: 25131 / Num. obs: 25131 / % possible obs: 95.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.082 / Χ2: 1.064 / Net I/σ(I): 18
Reflection shellResolution: 1.58→1.61 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.188 / Num. unique all: 1176 / Χ2: 1.09 / % possible all: 87.4

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å27.5 Å
Translation2.5 Å27.5 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-IceGUI interface to EPICS controldata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FVK

1fvk


Resolution: 1.58→21.058 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.888 / SU ML: 0.19 / σ(F): 1.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.189 1279 5.1 %RANDOM
Rwork0.145 ---
all0.1474 25131 --
obs0.147 25095 95.23 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.27 Å2 / ksol: 0.409 e/Å3
Displacement parametersBiso max: 53.6 Å2 / Biso mean: 16.954 Å2 / Biso min: 6.17 Å2
Baniso -1Baniso -2Baniso -3
1--10.546 Å20 Å2-0.442 Å2
2--8.339 Å2-0 Å2
3---2.207 Å2
Refinement stepCycle: LAST / Resolution: 1.58→21.058 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1450 0 0 259 1709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051559
X-RAY DIFFRACTIONf_angle_d0.9032126
X-RAY DIFFRACTIONf_chiral_restr0.059235
X-RAY DIFFRACTIONf_plane_restr0.004280
X-RAY DIFFRACTIONf_dihedral_angle_d18.199567
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.58-1.6430.1741410.10825882729258892
1.643-1.7180.1471350.10827082843270898
1.718-1.8090.1831450.10626712816267198
1.809-1.9220.1761470.11427072854270798
1.922-2.070.1711510.11927372888273798
2.07-2.2780.211370.12527232860272398
2.278-2.6070.1841460.14127272873272798
2.607-3.2830.1991390.15526972836269796
3.283-21.0590.1881380.17722582396225880

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