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- PDB-4h56: Crystal structure of the Clostridium perfringens NetB toxin in th... -

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Basic information

Entry
Database: PDB / ID: 4h56
TitleCrystal structure of the Clostridium perfringens NetB toxin in the membrane inserted form
ComponentsNecrotic enteritis toxin B
KeywordsTOXIN / Beta barrel / Pore forming toxin / Necrotic Enteritis / extracellular and membrane
Function / homology
Function and homology information


hemolysis in another organism / extracellular region / metal ion binding
Similarity search - Function
Leukocidin/porin MspA / Leukocidin-like / Bi-component toxin, staphylococci / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesClostridium perfringens (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.9 Å
AuthorsSavva, C.G. / Fernandes da Costa, S.P. / Bokori-Brown, M. / Naylor, C. / Cole, A.R. / Moss, D.S. / Titball, R.W. / Basak, A.K.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Molecular Architecture and Functional Analysis of NetB, a Pore-forming Toxin from Clostridium perfringens.
Authors: Savva, C.G. / Fernandes da Costa, S.P. / Bokori-Brown, M. / Naylor, C.E. / Cole, A.R. / Moss, D.S. / Titball, R.W. / Basak, A.K.
History
DepositionSep 18, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Mar 6, 2013Group: Database references
Revision 1.3Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Necrotic enteritis toxin B
B: Necrotic enteritis toxin B
C: Necrotic enteritis toxin B
D: Necrotic enteritis toxin B
E: Necrotic enteritis toxin B
F: Necrotic enteritis toxin B
G: Necrotic enteritis toxin B
H: Necrotic enteritis toxin B
I: Necrotic enteritis toxin B
J: Necrotic enteritis toxin B
K: Necrotic enteritis toxin B
L: Necrotic enteritis toxin B
M: Necrotic enteritis toxin B
N: Necrotic enteritis toxin B


Theoretical massNumber of molelcules
Total (without water)469,11514
Polymers469,11514
Non-polymers00
Water0
1
A: Necrotic enteritis toxin B
B: Necrotic enteritis toxin B
C: Necrotic enteritis toxin B
D: Necrotic enteritis toxin B
E: Necrotic enteritis toxin B
F: Necrotic enteritis toxin B
G: Necrotic enteritis toxin B


Theoretical massNumber of molelcules
Total (without water)234,5587
Polymers234,5587
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28980 Å2
ΔGint-75 kcal/mol
Surface area75210 Å2
MethodPISA
2
H: Necrotic enteritis toxin B
I: Necrotic enteritis toxin B
J: Necrotic enteritis toxin B
K: Necrotic enteritis toxin B
L: Necrotic enteritis toxin B
M: Necrotic enteritis toxin B
N: Necrotic enteritis toxin B


Theoretical massNumber of molelcules
Total (without water)234,5587
Polymers234,5587
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area29880 Å2
ΔGint-73 kcal/mol
Surface area74200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)313.230, 168.040, 160.460
Angle α, β, γ (deg.)90.00, 109.42, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A and (resseq 25:291 ) and (not element H)
21chain B and (resseq 25:291 ) and (not element H)
31chain C and (resseq 25:291 ) and (not element H)
41chain D and (resseq 25:291 ) and (not element H)
51chain E and (resseq 25:291 ) and (not element H)
61chain F and (resseq 25:291 ) and (not element H)
71chain G and (resseq 25:291 ) and (not element H)
81chain H and (resseq 25:291 ) and (not element H)
91chain I and (resseq 25:291 ) and (not element H)
101chain J and (resseq 25:291 ) and (not element H)
111chain K and (resseq 25:291 ) and (not element H)
121chain L and (resseq 25:291 ) and (not element H)
131chain M and (resseq 25:291 ) and (not element H)
141chain N and (resseq 25:291 ) and (not element H)

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 25:291 ) and (not element H)A0
211chain B and (resseq 25:291 ) and (not element H)B0
311chain C and (resseq 25:291 ) and (not element H)C0
411chain D and (resseq 25:291 ) and (not element H)D0
511chain E and (resseq 25:291 ) and (not element H)E0
611chain F and (resseq 25:291 ) and (not element H)F0
711chain G and (resseq 25:291 ) and (not element H)G0
811chain H and (resseq 25:291 ) and (not element H)H0
911chain I and (resseq 25:291 ) and (not element H)I0
1011chain J and (resseq 25:291 ) and (not element H)J0
1111chain K and (resseq 25:291 ) and (not element H)K0
1211chain L and (resseq 25:291 ) and (not element H)L0
1311chain M and (resseq 25:291 ) and (not element H)M0
1411chain N and (resseq 25:291 ) and (not element H)N0

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Components

#1: Protein
Necrotic enteritis toxin B / NetB


Mass: 33508.238 Da / Num. of mol.: 14 / Fragment: NetB mature toxin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium perfringens (bacteria) / Strain: 56 / Gene: netB / Plasmid: pHis Parallel II / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A8ULG6

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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: 4.24 Å3/Da / Density % sol: 71.02 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 12% PEG 4000, 100 mM Sodium cacodylate, 0.1 mM Polyethylene glycol dodecyl ether , pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Mar 12, 2012
RadiationMonochromator: Rigaku Osmic Varimax / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.9→27.7 Å / Num. all: 71370 / Num. obs: 69515 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 40.9 Å2 / Rmerge(I) obs: 0.344 / Net I/σ(I): 3.7
Reflection shellResolution: 3.9→4.11 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.685 / Mean I/σ(I) obs: 2 / Num. unique all: 10078 / % possible all: 97

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Processing

Software
NameVersionClassification
StructureStudiodata collection
PHASERMRphasing
PHENIX(phenix.refine: 1.8_1069)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 7AHL

7ahl


Resolution: 3.9→27.7 Å / SU ML: 0.68 / σ(F): 1.42 / Phase error: 32.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3089 3245 5.08 %RANDOM
Rwork0.2838 ---
obs0.2851 63875 89.56 %-
all-67120 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms27963 0 0 0 27963
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00328574
X-RAY DIFFRACTIONf_angle_d0.83239015
X-RAY DIFFRACTIONf_dihedral_angle_d15.2259631
X-RAY DIFFRACTIONf_chiral_restr0.0524324
X-RAY DIFFRACTIONf_plane_restr0.0035148
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1959X-RAY DIFFRACTIONPOSITIONAL0.007
12B1959X-RAY DIFFRACTIONPOSITIONAL0.007
13C1969X-RAY DIFFRACTIONPOSITIONAL0.006
14D1957X-RAY DIFFRACTIONPOSITIONAL0.009
15E1942X-RAY DIFFRACTIONPOSITIONAL0.006
16F1944X-RAY DIFFRACTIONPOSITIONAL0.008
17G1964X-RAY DIFFRACTIONPOSITIONAL0.009
18H1962X-RAY DIFFRACTIONPOSITIONAL0.006
19I1970X-RAY DIFFRACTIONPOSITIONAL0.009
110J1977X-RAY DIFFRACTIONPOSITIONAL0.007
111K1970X-RAY DIFFRACTIONPOSITIONAL0.008
112L1980X-RAY DIFFRACTIONPOSITIONAL0.006
113M1961X-RAY DIFFRACTIONPOSITIONAL0.008
114N1979X-RAY DIFFRACTIONPOSITIONAL0.006
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9-3.95810.49511120.4752288X-RAY DIFFRACTION77
3.9581-4.01980.5534780.50091459X-RAY DIFFRACTION50
4.0198-4.08550.4351470.37352437X-RAY DIFFRACTION85
4.0855-4.15570.3581350.35182436X-RAY DIFFRACTION84
4.1557-4.2310.35271350.32812494X-RAY DIFFRACTION84
4.231-4.31210.34761400.29452666X-RAY DIFFRACTION91
4.3121-4.39980.27921310.29212734X-RAY DIFFRACTION94
4.3998-4.4950.32531310.29222658X-RAY DIFFRACTION91
4.495-4.59920.29051250.27522546X-RAY DIFFRACTION85
4.5992-4.71360.28311360.23072654X-RAY DIFFRACTION90
4.7136-4.84040.25491490.24142697X-RAY DIFFRACTION92
4.8404-4.98210.24191460.24792722X-RAY DIFFRACTION93
4.9821-5.14190.25711470.2442756X-RAY DIFFRACTION93
5.1419-5.32440.29181380.24952737X-RAY DIFFRACTION93
5.3244-5.5360.29211540.27932761X-RAY DIFFRACTION93
5.536-5.78580.33691500.27432760X-RAY DIFFRACTION94
5.7858-6.08780.31241810.28432744X-RAY DIFFRACTION95
6.0878-6.46460.31931450.27832813X-RAY DIFFRACTION95
6.4646-6.95650.31191540.28932807X-RAY DIFFRACTION95
6.9565-7.64320.29261410.26052817X-RAY DIFFRACTION95
7.6432-8.71890.25021660.22292811X-RAY DIFFRACTION96
8.7189-10.87340.21521470.19912895X-RAY DIFFRACTION97
10.8734-27.71430.27111570.24022938X-RAY DIFFRACTION97

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