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- PDB-4ilf: Crystal structure of DsbC R125A from Salmonella enterica serovar ... -

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Basic information

Entry
Database: PDB / ID: 4ilf
TitleCrystal structure of DsbC R125A from Salmonella enterica serovar Typhimurium
ComponentsThiol:disulfide interchange protein DsbC
KeywordsISOMERASE / CXXC motif / disulfide isomerase
Function / homology
Function and homology information


Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / 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 / Thioredoxin, conserved site / Thioredoxin family active site. / Nuclear Transport Factor 2; Chain: A, ...Disulphide bond isomerase, DsbC/G, N-terminal / Disulfide bond isomerase protein N-terminal domain / 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 / Thioredoxin, conserved site / Thioredoxin family active site. / 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 DsbC
Similarity search - Component
Biological speciesSalmonella typhimurium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.999 Å
AuthorsHa, N.C. / Li, J. / Kim, J.S. / Yoon, B.Y. / Yeom, J.H. / Lee, K.
CitationJournal: J.Struct.Biol. / Year: 2013
Title: Crystal structure of the periplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium and the mechanistic implications.
Authors: Jiao, L. / Kim, J.S. / Song, W.S. / Yoon, B.Y. / Lee, K. / Ha, N.C.
History
DepositionDec 31, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 16, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein DsbC
B: Thiol:disulfide interchange protein DsbC


Theoretical massNumber of molelcules
Total (without water)48,2952
Polymers48,2952
Non-polymers00
Water12,809711
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint-14 kcal/mol
Surface area21130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.261, 79.193, 85.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Thiol:disulfide interchange protein DsbC / DsbC


Mass: 24147.646 Da / Num. of mol.: 2 / Mutation: R125A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella typhimurium (bacteria) / Strain: LT2 / SGSC1412 / ATCC 700720 / Gene: dsbC, STM3043 / Production host: Escherichia coli (E. coli) / References: UniProt: P55890
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 711 / Source method: isolated from a natural source / Formula: H2O

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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: 2.76 Å3/Da / Density % sol: 55.37 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M Litium sulfate, 0.1M Tris (pH 8.5), 32% PEG 4K, VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1.28248 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jul 23, 2012
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.28248 Å / Relative weight: 1
ReflectionResolution: 1.999→19.958 Å / Num. all: 36760 / Num. obs: 33580 / % possible obs: 91.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2-2.03186.1
2.03-2.07192.1
2.07-2.11190.7
2.11-2.15191.1
2.15-2.2192.8
2.2-2.25192.4
2.25-2.31191.8
2.31-2.37191.7
2.37-2.44190.7
2.44-2.52190.9
2.52-2.61190.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8.1_1168)refinement
DENZOdata reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.999→19.958 Å / SU ML: 0.23 / σ(F): 1.5 / Phase error: 19.94 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2277 1988 5.92 %RANDOM
Rwork0.1772 ---
all0.1802 33598 --
obs0.1802 30371 91.35 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.999→19.958 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3294 0 0 711 4005
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073360
X-RAY DIFFRACTIONf_angle_d1.0454544
X-RAY DIFFRACTIONf_dihedral_angle_d14.9081237
X-RAY DIFFRACTIONf_chiral_restr0.069513
X-RAY DIFFRACTIONf_plane_restr0.004587
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9992-2.04910.30491350.2558216689
2.0491-2.10450.27191370.2448220291
2.1045-2.16630.29971470.2264222191
2.1663-2.23620.28991350.2095226893
2.2362-2.3160.25651470.2062223692
2.316-2.40860.25121350.1993224391
2.4086-2.5180.24241450.1879222691
2.518-2.65050.24481380.1845223791
2.6505-2.81610.24791380.1823223491
2.8161-3.03280.2461440.1755224191
3.0328-3.33680.23421390.1644232193
3.3368-3.81670.1771550.1446232294
3.8167-4.79760.18151450.1345230891
4.7976-19.95870.19351480.1652236790

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