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- PDB-3l9u: Crystal Structure of Salmonella enterica serovar Typhimurium DsbL -

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Basic information

Entry
Database: PDB / ID: 3l9u
TitleCrystal Structure of Salmonella enterica serovar Typhimurium DsbL
ComponentsDisulfide isomerase
KeywordsOXIDOREDUCTASE / thioredoxin-fold / DsbL / thiol-disulfide oxidoreductase / Isomerase
Function / homology
Function and homology information


protein-disulfide reductase activity / isomerase activity / periplasmic space
Similarity search - Function
Thiol:disulfide interchange protein DsbL / Thiol:disulphide interchange protein DsbA/DsbL / : / DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Thiol:disulfide interchange protein DsbL / Thiol:disulfide interchange protein DsbL
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.568 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 9, 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: Disulfide isomerase


Theoretical massNumber of molelcules
Total (without water)22,2261
Polymers22,2261
Non-polymers00
Water5,386299
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)85.582, 46.593, 60.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-288-

HOH

21A-298-

HOH

31A-300-

HOH

41A-427-

HOH

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Components

#1: Protein Disulfide isomerase / Thiol:disulfide interchange protein DsbL


Mass: 22226.443 Da / Num. of mol.: 1 / Fragment: UNP residues 25-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)
Strain: SL1344 / Gene: dsbL, STM3193 / Plasmid: pETLIC / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3)/plyss
References: UniProt: E1WHY0, UniProt: Q8ZLZ0*PLUS, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 299 / 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: 2.7 Å3/Da / Density % sol: 54.46 % / Mosaicity: 0.418 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 2.6-3.4 M sodium malonate pH 7.0 -7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.956667 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 15, 2008 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.956667 Å / Relative weight: 1
ReflectionResolution: 1.568→50 Å / Num. all: 34491 / Num. obs: 34491 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Rmerge(I) obs: 0.066 / Χ2: 1.056 / Net I/σ(I): 10.6
Reflection shellResolution: 1.57→1.6 Å / Redundancy: 7 % / Rmerge(I) obs: 0.459 / Mean I/σ(I) obs: 4.12 / Num. unique all: 1693 / Χ2: 0.92 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
Blu-IceGUI interface to EPICS controldata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3C7M

3c7m


Resolution: 1.568→28.404 Å / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.903 / SU ML: 0.13 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.184 1745 5.07 %RANDOM
Rwork0.15 ---
all0.152 34491 --
obs0.152 34443 99.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.469 Å2 / ksol: 0.413 e/Å3
Displacement parametersBiso max: 58.83 Å2 / Biso mean: 19.668 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1-6.903 Å2-0 Å2-0 Å2
2---1.867 Å20 Å2
3----5.036 Å2
Refinement stepCycle: LAST / Resolution: 1.568→28.404 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1553 0 0 299 1852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061655
X-RAY DIFFRACTIONf_angle_d0.9442245
X-RAY DIFFRACTIONf_chiral_restr0.065243
X-RAY DIFFRACTIONf_plane_restr0.004286
X-RAY DIFFRACTIONf_dihedral_angle_d17.42603
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
1.568-1.6240.2171550.13932053360320599
1.624-1.6890.1651800.131321133913211100
1.689-1.7660.1941740.129323334073233100
1.766-1.8590.1751700.126323234023232100
1.859-1.9760.1621760.125322534013225100
1.976-2.1280.1761850.126326334483263100
2.128-2.3420.1641530.133328434373284100
2.342-2.6810.1921800.16327234523272100
2.681-3.3770.2091960.159331035063310100
3.377-28.4090.1561760.14834633639346399

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