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- PDB-4mly: Disulfide isomerase from multidrug resistance IncA/C related inte... -

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Basic information

Entry
Database: PDB / ID: 4mly
TitleDisulfide isomerase from multidrug resistance IncA/C related integrative and conjugative elements in oxidized state (P21 space group)
ComponentsDsbP
KeywordsISOMERASE / DsbC / DsbG / folding and assembly / bacterial conjugation / horizontal gene transfer / domain swapping / thioredoxin fold / bacterial periplasmic space
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 domain superfamily / Disulphide bond isomerase, DsbC/G / Thioredoxin-like domain / Thioredoxin-like fold / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
1,3-BUTANEDIOL / Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesProteus mirabilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.207 Å
AuthorsPremkumar, L. / Kurth, F. / Neyer, S. / Martin, J.L.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Multidrug Resistance IncA/C Transferable Plasmid Encodes a Novel Domain-swapped Dimeric Protein-disulfide Isomerase.
Authors: Premkumar, L. / Kurth, F. / Neyer, S. / Schembri, M.A. / Martin, J.L.
History
DepositionSep 6, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Feb 19, 2014Group: Database references
Revision 1.3Nov 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: DsbP
B: DsbP
C: DsbP
D: DsbP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9607
Polymers95,6904
Non-polymers2703
Water6,377354
1
A: DsbP
D: DsbP


Theoretical massNumber of molelcules
Total (without water)47,8452
Polymers47,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-16 kcal/mol
Surface area20510 Å2
MethodPISA
2
B: DsbP
C: DsbP
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1155
Polymers47,8452
Non-polymers2703
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4550 Å2
ΔGint-12 kcal/mol
Surface area20870 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16110 Å2
ΔGint-56 kcal/mol
Surface area34200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.580, 110.460, 74.100
Angle α, β, γ (deg.)90.00, 93.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
DsbP / DsbP thiol:disulfide interchange protein / plasmid or integrative and conjugative elements encoded ...DsbP thiol:disulfide interchange protein / plasmid or integrative and conjugative elements encoded disulfide isomerase


Mass: 23922.439 Da / Num. of mol.: 4 / Fragment: UNP residues 22-235
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Proteus mirabilis (bacteria) / Gene: dsbC, DsbP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: D0FZX2, protein disulfide-isomerase
#2: Chemical ChemComp-BU2 / 1,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 354 / 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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 10% PEG4000, 20% v/v glycerol, 0.1 M MES/imidazole, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol (racemic), 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol , pH ...Details: 10% PEG4000, 20% v/v glycerol, 0.1 M MES/imidazole, 20 mM 1,6-hexanediol, 20 mM 1-butanol, 20 mM 1,2-propanediol (racemic), 20 mM 2-propanol, 20 mM 1,4-butanediol, 20 mM 1,3-propanediol , pH 6.5, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Aug 25, 2012
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.207→42.79 Å / Num. all: 43861 / Num. obs: 43861 / % possible obs: 99.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.5 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 16.2
Reflection shellResolution: 2.207→2.27 Å / Redundancy: 4 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 5 / Num. unique all: 3564 / % possible all: 93.4

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.207→35.081 Å / SU ML: 0.27 / σ(F): 0 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2338 2227 5.08 %RANDOM
Rwork0.1862 ---
all0.1887 43816 --
obs0.1887 43816 99.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.207→35.081 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6163 0 18 354 6535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0156373
X-RAY DIFFRACTIONf_angle_d1.5128604
X-RAY DIFFRACTIONf_dihedral_angle_d12.5192398
X-RAY DIFFRACTIONf_chiral_restr0.061975
X-RAY DIFFRACTIONf_plane_restr0.0091114
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.207-2.2550.33961180.27332406X-RAY DIFFRACTION92
2.255-2.30740.3021450.24282551X-RAY DIFFRACTION99
2.3074-2.36510.28461260.21772613X-RAY DIFFRACTION100
2.3651-2.42910.26421480.21462593X-RAY DIFFRACTION100
2.4291-2.50050.2821350.20142626X-RAY DIFFRACTION100
2.5005-2.58120.29391260.20892602X-RAY DIFFRACTION100
2.5812-2.67340.26041410.2052605X-RAY DIFFRACTION100
2.6734-2.78040.25651440.20612611X-RAY DIFFRACTION100
2.7804-2.90690.26531410.19782618X-RAY DIFFRACTION100
2.9069-3.06010.24861370.20352614X-RAY DIFFRACTION100
3.0601-3.25170.23021460.19692611X-RAY DIFFRACTION100
3.2517-3.50250.22831460.18282608X-RAY DIFFRACTION100
3.5025-3.85460.23231530.17232601X-RAY DIFFRACTION100
3.8546-4.41150.19981320.15162645X-RAY DIFFRACTION100
4.4115-5.55440.1911520.15272625X-RAY DIFFRACTION100
5.5544-35.0850.22331370.19452660X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4571-1.95820.26663.5929-1.7671.21790.13490.31-0.1825-0.27110.050.41950.0478-0.1799-0.13320.2256-0.0697-0.05330.24540.0020.2741-9.13354.5599-37.8223
21.52160.139-1.74051.40160.13783.8457-0.18460.1824-0.1397-0.361-0.0704-0.10180.45230.1520.24460.3422-0.0349-0.00470.51170.0440.2743-12.8706-19.5876-44.4515
33.34830.44410.68940.8932-0.09461.8652-0.0844-0.37960.46140.16640.12350.0789-0.2302-0.1917-0.03090.27060.00930.0440.2635-0.10470.2665-10.4786-2.2864-10.0123
43.6602-0.41720.26132.20590.06661.79670.0611-0.5468-0.95710.2827-0.01860.26770.3515-0.2524-0.01020.2673-0.0896-0.03990.15690.06240.4182-7.7465-25.2305-15.219
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'

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