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- PDB-4ml1: Disulfide isomerase (DsbP) from multidrug resistance IncA/C trans... -

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Basic information

Entry
Database: PDB / ID: 4ml1
TitleDisulfide isomerase (DsbP) from multidrug resistance IncA/C transferable plasmid in oxidized state (P212121 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


isomerase activity / periplasmic space
Similarity search - Function
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
Thiol:disulfide interchange protein
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.978 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


Theoretical massNumber of molelcules
Total (without water)95,6904
Polymers95,6904
Non-polymers00
Water12,376687
1
A: DsbP
B: DsbP


Theoretical massNumber of molelcules
Total (without water)47,8452
Polymers47,8452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-21 kcal/mol
Surface area21240 Å2
MethodPISA
2
C: 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 area4140 Å2
ΔGint-21 kcal/mol
Surface area21170 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14970 Å2
ΔGint-77 kcal/mol
Surface area35760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.330, 108.270, 139.020
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
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.) Klebsiella pneumoniae (bacteria) / Gene: dsbC, DsbP, pNDM10469_89 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLys / References: UniProt: A6GV51, protein disulfide-isomerase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 687 / 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: 2.14 Å3/Da / Density % sol: 42.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 15% PEG3350, 0.1 M sodium malonate, pH 6.6, 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: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.978→54.14 Å / Num. all: 58014 / Num. obs: 58014 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.079 / Net I/σ(I): 8.9
Reflection shellResolution: 1.978→2.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.465 / Mean I/σ(I) obs: 2.5 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Blu-IceICEdata collection
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.978→50.603 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 23.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2425 2926 5.07 %
Rwork0.1918 --
obs0.1944 57720 99.25 %
all-57719 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.978→50.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 0 687 6948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0146401
X-RAY DIFFRACTIONf_angle_d1.4688635
X-RAY DIFFRACTIONf_dihedral_angle_d12.462407
X-RAY DIFFRACTIONf_chiral_restr0.063978
X-RAY DIFFRACTIONf_plane_restr0.0091117
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.978-2.01040.29181430.23562579X-RAY DIFFRACTION99
2.0104-2.04510.31141360.23142555X-RAY DIFFRACTION99
2.0451-2.08230.28561400.23272543X-RAY DIFFRACTION99
2.0823-2.12240.30371390.22672573X-RAY DIFFRACTION99
2.1224-2.16570.28361310.21372618X-RAY DIFFRACTION100
2.1657-2.21280.26911380.21332554X-RAY DIFFRACTION100
2.2128-2.26420.47171360.39392412X-RAY DIFFRACTION92
2.2642-2.32090.28171640.23242545X-RAY DIFFRACTION99
2.3209-2.38360.29281420.20372615X-RAY DIFFRACTION100
2.3836-2.45380.23871310.18852614X-RAY DIFFRACTION100
2.4538-2.5330.26391610.18712575X-RAY DIFFRACTION100
2.533-2.62350.24991240.19262627X-RAY DIFFRACTION100
2.6235-2.72850.26151370.19612621X-RAY DIFFRACTION100
2.7285-2.85270.26441360.1882627X-RAY DIFFRACTION100
2.8527-3.00310.24531100.19482652X-RAY DIFFRACTION100
3.0031-3.19120.2831410.19192639X-RAY DIFFRACTION100
3.1912-3.43750.22591460.18692609X-RAY DIFFRACTION100
3.4375-3.78340.21161480.17432642X-RAY DIFFRACTION100
3.7834-4.33060.19491370.15362666X-RAY DIFFRACTION99
4.3306-5.4550.17431410.14292698X-RAY DIFFRACTION99
5.455-50.61950.19721450.17832830X-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)
12.62060.5108-0.51421.1458-0.61391.73410.0895-0.5917-0.04190.2037-0.04340.08060.025-0.0278-0.03130.20790.0013-0.0390.2368-0.02420.180113.2064-8.7959-29.1637
21.9721-0.50410.64651.5164-0.54941.24090.03820.34210.2445-0.27440.00420.0885-0.0789-0.02080.13240.23480.01840.06030.24060.02590.20412.74669.6742-62.3632
30.37551.43820.81611.81591.08370.77290.0659-0.0092-0.14380.01680.0384-0.2028-0.00970.0746-0.08570.1821-0.00280.05950.2474-0.09830.27811.876315.0036-33.0131
42.6646-0.3238-0.36961.70310.72881.15550.05160.2527-0.3473-0.1318-0.0108-0.10220.09720.00270.12860.180.003-0.05730.1494-0.02510.13118.6341-13.7926-57.936
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 212 )
2X-RAY DIFFRACTION2chain 'B' and (resid 10 through 213 )
3X-RAY DIFFRACTION3chain 'C' and (resid 12 through 213 )
4X-RAY DIFFRACTION4chain 'D' and (resid 11 through 213 )

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