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- PDB-4phq: ClyA CC6/264 ox (6-303) -

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Basic information

Entry
Database: PDB / ID: 4phq
TitleClyA CC6/264 ox (6-303)
ComponentsHemolysin E, chromosomal
KeywordsTOXIN / alpha pore-forming toxin / intramolecular disulfide bond
Function / homology
Function and homology information


modulation of apoptotic process in another organism / hemolysis in another organism / toxin activity / periplasmic space / host cell plasma membrane / extracellular region / membrane / identical protein binding
Similarity search - Function
Hemolysin E; Chain: A; / Hemolysin E; Chain: A; - #10 / Hemolysin E / Haemolysin E (HlyE) / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / Hemolysin E, chromosomal
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.94 Å
AuthorsRoderer, D.J.A. / Glockshuber, R. / Ban, N.
CitationJournal: Biochemistry / Year: 2014
Title: Characterization of Variants of the Pore-Forming Toxin ClyA from Escherichia coli Controlled by a Redox Switch.
Authors: Roderer, D. / Benke, S. / Muller, M. / Fah-Rechsteiner, H. / Ban, N. / Schuler, B. / Glockshuber, R.
History
DepositionMay 6, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2014Group: Database references
Revision 1.2Oct 29, 2014Group: Database references
Revision 1.3Dec 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin E, chromosomal
B: Hemolysin E, chromosomal
C: Hemolysin E, chromosomal
D: Hemolysin E, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,03118
Polymers132,7754
Non-polymers1,25614
Water11,349630
1
A: Hemolysin E, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4704
Polymers33,1941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hemolysin E, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4704
Polymers33,1941
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Hemolysin E, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,7467
Polymers33,1941
Non-polymers5536
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Hemolysin E, chromosomal
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3453
Polymers33,1941
Non-polymers1512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)176.880, 48.440, 152.430
Angle α, β, γ (deg.)90.000, 102.330, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is a monomer

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Components

#1: Protein
Hemolysin E, chromosomal / Cytotoxin ClyA / Hemolysis-inducing protein / Latent pore-forming 34 kDa hemolysin / Silent hemolysin SheA


Mass: 33193.664 Da / Num. of mol.: 4 / Mutation: delta 1-5, A6C, V264C, C87A, C285A
Source method: isolated from a genetically manipulated source
Details: 5 Quick-change PCRs to introduce point mutations and delete N-terminal residues, TEV cleavage of N-terminal His(6)-tag
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: hlyE, clyA, hpr, sheA, ycgD, b1182, JW5181 / Plasmid: pET11a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Tuner / References: UniProt: P77335
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 630 / 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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.7 / Details: 19% PEG 3350, 0.1 M Tris-Acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 15, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.94→40 Å / Num. obs: 86049 / % possible obs: 91.4 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 24.23 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.076 / Rrim(I) all: 0.084 / Χ2: 0.959 / Net I/σ(I): 14.53 / Num. measured all: 511121
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.94-2.060.8670.5273.277859815307138240.57990.3
2.06-2.20.9470.3355.258032614031132710.36694.6
2.2-2.370.9720.218.017163012783119250.2393.3
2.37-2.60.9860.13311.536229812519109170.14687.2
2.6-2.90.9930.09716.026472510900104440.10695.8
2.9-3.350.9960.06821.3256040991992140.07492.9
3.35-4.10.9980.04628.9341243840973350.0587.2
4.1-5.760.9980.03835.5836869650060370.04292.9
5.760.9990.03240.0719392381030820.03580.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.58 Å39.55 Å
Translation2.58 Å39.55 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QOY

1qoy


Resolution: 1.94→38.54 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 22.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2137 1917 2.32 %
Rwork0.1721 80705 -
obs0.1731 82622 87.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.24 Å2 / Biso mean: 32.1716 Å2 / Biso min: 5.98 Å2
Refinement stepCycle: final / Resolution: 1.94→38.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9085 0 82 630 9797
Biso mean--40.43 34.33 -
Num. residues----1158
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079405
X-RAY DIFFRACTIONf_angle_d0.89712688
X-RAY DIFFRACTIONf_chiral_restr0.061474
X-RAY DIFFRACTIONf_plane_restr0.0031605
X-RAY DIFFRACTIONf_dihedral_angle_d15.1953507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9398-1.98830.3321140.24564698X-RAY DIFFRACTION73
1.9883-2.0420.32531450.22695472X-RAY DIFFRACTION84
2.042-2.10210.2911540.21555697X-RAY DIFFRACTION87
2.1021-2.170.25641440.19235750X-RAY DIFFRACTION89
2.17-2.24750.26541240.17565836X-RAY DIFFRACTION89
2.2475-2.33750.21851270.17695904X-RAY DIFFRACTION90
2.3375-2.44380.22591250.16835779X-RAY DIFFRACTION88
2.4438-2.57270.19731320.17395336X-RAY DIFFRACTION82
2.5727-2.73380.24251550.1766214X-RAY DIFFRACTION95
2.7338-2.94480.21891320.17376223X-RAY DIFFRACTION94
2.9448-3.2410.19261380.17186134X-RAY DIFFRACTION93
3.241-3.70970.20921400.16635510X-RAY DIFFRACTION83
3.7097-4.67250.1781560.14576300X-RAY DIFFRACTION95
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)
10.14580.15490.05250.51050.01750.83740.13170.0810.0336-0.0386-0.04530.0154-0.3304-0.230.01320.16250.0676-0.03470.10070.00840.1369-20.598878.3328191.2279
20.13530.2403-0.17910.3523-0.0441.28660.1235-0.01860.1589-0.1028-0.05950.0869-0.294-0.5568-0.07920.23660.2478-0.0291-0.03170.0090.1447-24.767180.6534185.9603
30.2269-0.01940.48360.67090.04571.0772-0.10580.0046-0.011-0.11480.0754-0.04710.26270.2997-0.00670.08650.0668-0.04160.1075-0.00350.120916.526298.703183.0854
40.78550.3556-0.33621.1069-0.31240.29910.0018-0.318-0.09780.3935-0.0735-0.04950.06130.25980.04070.29190.11440.02910.22450.07410.18339.630687.7463209.0793
50.9133-0.2416-0.47590.93050.06561.1434-0.21210.0111-0.17570.08910.00880.12190.3697-0.2679-0.06150.08750.0022-0.02990.0171-0.02470.1396-13.9712106.0517187.3832
60.7004-0.0338-0.51270.54240.22951.31160.03480.51790.0412-0.70170.04240.0447-0.295-0.38190.20870.3668-0.0468-0.01610.3574-0.08410.2022-10.0646104.8399157.2666
70.95040.2521-0.10560.58610.11010.81480.07020.33180.3485-0.04860.0209-0.0195-0.3350.26870.00690.143-0.0231-0.04710.40670.11540.2395-50.720988.9701183.3834
80.06950.0868-0.0140.15770.02890.0419-0.0439-0.4630.14910.6049-0.13830.4209-0.0337-0.2527-0.00090.42260.01470.08470.4768-0.10210.3555-80.204784.7534217.8494
90.34560.0280.19240.2091-0.03040.13960.0339-0.12030.5672-0.15360.0936-0.1666-0.20370.6304-0.01490.3033-0.15890.03590.57810.07710.3715-41.98292.7246183.3028
100.1417-0.0514-0.18880.0250.04830.30920.02820.1983-0.3462-0.02480.04350.09460.05690.3268-0.0270.04280.03250.00130.58990.08070.3193-35.661877.9284177.191
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 6:181)A6 - 181
2X-RAY DIFFRACTION2(chain A and resid 182:296)A182 - 298
3X-RAY DIFFRACTION3(chain B and resid 6:260)B6 - 260
4X-RAY DIFFRACTION4(chain B and resid 261:297)B261 - 298
5X-RAY DIFFRACTION5(chain C and resid 6:260)C6 - 260
6X-RAY DIFFRACTION6(chain C and resid 261:298)C261 - 298
7X-RAY DIFFRACTION7(chain D and resid 6:167)D6 - 167
8X-RAY DIFFRACTION8(chain D and resid 168:214)D168 - 214
9X-RAY DIFFRACTION9(chain D and resid 215:268)D215 - 268
10X-RAY DIFFRACTION10(chain D and resid 269:290)D269 - 298

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