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- PDB-4i5q: Crystal structure and catalytic mechanism for peroplasmic disulfi... -

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Basic information

Entry
Database: PDB / ID: 4i5q
TitleCrystal structure and catalytic mechanism for peroplasmic disulfide-bond isomerase DsbC from Salmonella enterica serovar Typhimurium
ComponentsThiol:disulfide interchange protein DsbC
KeywordsISOMERASE / CXXC Motif / disuflide isomerase / periplasmic
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: 1.962 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
DepositionNov 28, 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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)48,4923
Polymers48,4682
Non-polymers241
Water6,269348
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-23 kcal/mol
Surface area21400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.989, 78.526, 84.414
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


Mass: 24233.762 Da / Num. of mol.: 2
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: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 348 / 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: 2.67 Å3/Da / Density % sol: 53.87 %
Crystal growTemperature: 287.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.9M Sodium chloride, 0.1M Hepes(pH 7.0) , VAPOR DIFFUSION, HANGING DROP, temperature 287.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6C1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 9, 2011
RadiationMonochromator: double mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.962→50 Å / Num. all: 36553 / Num. obs: 36553 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.22-2.27197.5
2.17-2.22198.3
2.12-2.17197.3
2.08-2.12195.9
2.04-2.08196.3
2-2.04192.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
CCP4model building
PHENIX(phenix.refine: 1.8_1069)refinement
DENZOdata reduction
HKL-2000data scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 1.962→28.642 Å / SU ML: 0.29 / σ(F): 1.48 / Phase error: 26.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2544 1833 5.02 %RANDOM
Rwork0.2038 ---
all0.2063 36553 --
obs0.2063 36530 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.962→28.642 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 1 348 3661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083380
X-RAY DIFFRACTIONf_angle_d1.044566
X-RAY DIFFRACTIONf_dihedral_angle_d14.7741249
X-RAY DIFFRACTIONf_chiral_restr0.071514
X-RAY DIFFRACTIONf_plane_restr0.005590
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9624-2.01540.37671210.3354232885
2.0154-2.07470.35361430.3003255295
2.0747-2.14170.31481460.2696262896
2.1417-2.21820.31611280.2503268798
2.2182-2.3070.27571420.2372265998
2.307-2.41190.2771420.2293267498
2.4119-2.5390.33421410.2255266298
2.539-2.6980.26281460.2271271298
2.698-2.90610.31141400.2335270999
2.9061-3.19820.29941430.2195272899
3.1982-3.66020.22961350.184276499
3.6602-4.60830.21031590.1535278099
4.6083-28.64480.20611470.1814281496

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