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- PDB-5ew5: Crystal Structure of Colicin E9 In Complex with Its Immunity Prot... -

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Basic information

Entry
Database: PDB / ID: 5ew5
TitleCrystal Structure of Colicin E9 In Complex with Its Immunity Protein Im9
Components
  • Colicin-E9
  • Colicin-E9 immunity protein
KeywordsHYDROLASE / colicin / complex / toxin
Function / homology
Function and homology information


extrachromosomal circular DNA / bacteriocin immunity / nucleic acid phosphodiester bond hydrolysis / toxic substance binding / endonuclease activity / cytolysis / pathogenesis / Hydrolases, Acting on ester bonds / defense response to bacterium / protein domain specific binding ...extrachromosomal circular DNA / bacteriocin immunity / nucleic acid phosphodiester bond hydrolysis / toxic substance binding / endonuclease activity / cytolysis / pathogenesis / Hydrolases, Acting on ester bonds / defense response to bacterium / protein domain specific binding / protein-containing complex / metal ion binding
Colicin immunity protein/pyocin immunity protein / Pyosin/cloacin translocation domain superfamily / Cloacin colicin family / Colicin, receptor domain / Pyosin/cloacin translocation domain / HNH nuclease / Colicin/pyocin, DNase domain superfamily / Colicin immunity protein / pyocin immunity protein / Colicin-like bacteriocin tRNase domain / Coiled-coil receptor-binding R-domain of colicin E2 / Colicin E immunity protein superfamily
Colicin-E9 / Colicin-E9 immunity protein
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsKlein, A. / Wojdyla, J.A. / Kleanthous, C.
CitationJournal: Biochem.J. / Year: 2016
Title: Structural and biophysical analysis of nuclease protein antibiotics.
Authors: Klein, A. / Wojdyla, J.A. / Joshi, A. / Josts, I. / McCaughey, L.C. / Housden, N.G. / Kaminska, R. / Byron, O. / Walker, D. / Kleanthous, C.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 20, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2016Group: Database references
Revision 1.2Sep 21, 2016Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Colicin-E9
B: Colicin-E9
C: Colicin-E9
D: Colicin-E9
E: Colicin-E9 immunity protein
F: Colicin-E9 immunity protein
G: Colicin-E9 immunity protein
H: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)288,9078
Polymers288,9078
Non-polymers00
Water39622
1
A: Colicin-E9
E: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)72,2272
Polymers72,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Colicin-E9
F: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)72,2272
Polymers72,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Colicin-E9
H: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)72,2272
Polymers72,2272
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Colicin-E9
G: Colicin-E9 immunity protein


Theoretical massNumber of molelcules
Total (without water)72,2272
Polymers72,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)94.894, 116.050, 150.365
Angle α, β, γ (deg.)90.00, 93.72, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D
13E
23F
14G
24H

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDAuth asym-IDAuth seq-ID
11A85 - 580
21B85 - 580
12C85 - 580
22D85 - 580
13E3 - 85
23F3 - 85
14G6 - 84
24H6 - 84

NCS ensembles:
ID
1
2
3
4

NCS oper:

Code: given

IDMatrixVector
1(1), (1), (1)
2(0.514385, -0.011156, -0.857487), (-0.010891, -0.99992, 0.006476), (-0.85749, 0.006008, -0.514465)-19.54343, -24.34243, -34.30386

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Components

#1: Protein/peptide
Colicin-E9


Mass: 61563.145 Da / Num. of mol.: 4 / Mutation: Y324C, L447C, D448A, K449M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: col, cei / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: P09883, Hydrolases, Acting on ester bonds
#2: Protein/peptide
Colicin-E9 immunity protein / ImmE9 / Microcin-E9 immunity protein


Mass: 10663.653 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: imm, ceiE9 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13479
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 22 / Source method: isolated from a natural source / Formula: H2O / Water

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 1.3M sodium malonate, PEG3350 / PH range: 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.2→29.6 Å / Num. obs: 53941 / % possible obs: 99.1 % / Redundancy: 3.5 % / Rsym value: 0.0127 / Net I/σ(I): 7.7
Reflection shellResolution: 3.2→3.3 Å / Redundancy: 3.37 % / Mean I/σ(I) obs: 1.8 / Rsym value: 0.694 / % possible all: 95.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JCH and 2GZG
Resolution: 3.2→29.6 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.894 / SU B: 31.06 / SU ML: 0.491 / Cross valid method: THROUGHOUT / ESU R Free: 0.519 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27062 2705 5.1 %RANDOM
Rwork0.21242 ---
Obs0.21544 50598 98.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.384 Å2
Baniso -1Baniso -2Baniso -3
1-6.09 Å20 Å2-7.09 Å2
2---2.04 Å20 Å2
3----3.1 Å2
Refinement stepCycle: 1 / Resolution: 3.2→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17364 0 0 22 17386
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.010.01917682
r_bond_other_d0.0010.0216851
r_angle_refined_deg1.311.95723921
r_angle_other_deg0.791338991
r_dihedral_angle_1_deg6.11152257
r_dihedral_angle_2_deg34.88625.267824
r_dihedral_angle_3_deg16.085153088
r_dihedral_angle_4_deg18.45815117
r_chiral_restr0.0670.22643
r_gen_planes_refined0.0050.02120302
r_gen_planes_other0.0010.023751
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it5.3729.119066
r_mcbond_other5.3699.119065
r_mcangle_it8.85313.65311310
r_mcangle_other8.85613.65311311
r_scbond_it5.2339.6878616
r_scbond_other5.2339.6878617
r_scangle_it
r_scangle_other8.8514.31612612
r_long_range_B_refined13.31671.52219772
r_long_range_B_other13.31871.52619770
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refinement-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A7396MEDIUM POSITIONAL0.120.5
1A7396MEDIUM THERMAL8.232
2C7372MEDIUM POSITIONAL0.10.5
2C7372MEDIUM THERMAL62
3E1251MEDIUM POSITIONAL0.080.5
3E1251MEDIUM THERMAL6.172
4G1034MEDIUM POSITIONAL0.160.5
4G1034MEDIUM THERMAL12.82
LS refinement shellResolution: 3.199→3.282 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.419 180 -
Rwork0.351 3540 -
Obs--93.4 %

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