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- PDB-3o44: Crystal Structure of the Vibrio cholerae Cytolysin (HlyA) Heptame... -

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Basic information

Entry
Database: PDB / ID: 3o44
TitleCrystal Structure of the Vibrio cholerae Cytolysin (HlyA) Heptameric Pore
ComponentsHemolysin
KeywordsTOXIN / pore-forming toxin / hemolysin / cytolysin / beta-barrel / channel / membrane protein / detergent-solubilized / liposome
Function / homology
Function and homology information


cytolysis in another organism / toxin activity / carbohydrate binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / host cell plasma membrane ...cytolysis in another organism / toxin activity / carbohydrate binding / tRNA binding / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / host cell plasma membrane / extracellular region / membrane / identical protein binding
Similarity search - Function
Leukocidin/Hemolysin toxin, pre-stem domain / Porin MspA ribbon fold / Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/porin MspA / Leukocidin-like ...Leukocidin/Hemolysin toxin, pre-stem domain / Porin MspA ribbon fold / Hemolytic toxin, N-terminal / Hemolytic toxin, N-terminal domain superfamily / Hemolysin, pre-stem domain / Hemolytic toxin N terminal / Hemolysin, beta-prism lectin / Beta-prism lectin / Leukocidin/porin MspA / Leukocidin-like / Leukocidin/Hemolysin toxin / Leukocidin/Hemolysin toxin family / Leukocidin/porin MspA superfamily / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain superfamily / Ricin-type beta-trefoil / Other non-globular / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Ribosomal protein L5, bacterial-type / Distorted Sandwich / Special / Ribosomal protein L5, conserved site / Ribosomal protein L5, N-terminal / Ribosomal protein L5 signature. / Ribosomal protein L5, C-terminal / Ribosomal protein L5 / Ribosomal protein L5 domain superfamily / Ribosomal protein L5 / ribosomal L5P family C-terminus / Mainly Beta
Similarity search - Domain/homology
Large ribosomal subunit protein uL5 / Hemolysin
Similarity search - Component
Biological speciesVibrio cholerae 12129
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.88 Å
AuthorsDe, S. / Olson, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystal structure of the Vibrio cholerae cytolysin heptamer reveals common features among disparate pore-forming toxins.
Authors: De, S. / Olson, R.
History
DepositionJul 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)920,09714
Polymers920,09714
Non-polymers00
Water11,710650
1
A: Hemolysin
B: Hemolysin
C: Hemolysin
D: Hemolysin
E: Hemolysin
F: Hemolysin
G: Hemolysin


Theoretical massNumber of molelcules
Total (without water)460,0497
Polymers460,0497
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
H: Hemolysin
I: Hemolysin
J: Hemolysin
K: Hemolysin
L: Hemolysin
M: Hemolysin
N: Hemolysin


Theoretical massNumber of molelcules
Total (without water)460,0497
Polymers460,0497
Non-polymers00
Water1267
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)172.354, 182.859, 430.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L
131M
141N
12B
22C
32D
42E
52F
62G
72H
82I
92J
102K
112M
122N
13A
23L

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resid 135:588)A135 - 588
211chain B and (resid 135:588)B135 - 588
311chain C and (resid 135:588)C135 - 588
411chain D and (resid 135:588)D135 - 588
511chain E and (resid 135:588)E135 - 588
611chain F and (resid 135:588)F135 - 588
711chain G and (resid 135:588)G135 - 588
811chain H and (resid 135:588)H135 - 588
911chain I and (resid 135:588)I135 - 588
1011chain J and (resid 135:588)J135 - 588
1111chain K and (resid 135:588)K135 - 588
1211chain L and (resid 135:588)L135 - 588
1311chain M and (resid 135:588)M135 - 588
1411chain N and (resid 135:588)N135 - 588
112chain B and resid 589:716B589 - 716
212chain C and resid 589:716C589 - 716
312chain D and resid 589:716D589 - 716
412chain E and resid 589:716E589 - 716
512chain F and resid 589:716F589 - 716
612chain G and resid 589:716G589 - 716
712chain H and resid 589:716H589 - 716
812chain I and resid 589:716I589 - 716
912chain J and resid 589:716J589 - 716
1012chain K and resid 589:716K589 - 716
1112chain M and resid 589:716M589 - 716
1212chain N and resid 589:716N589 - 716
113chain A and resid 589:716A589 - 716
213chain L and resid 589:716L589 - 716

NCS ensembles :
ID
1
2
3

NCS oper:
IDCodeMatrixVector
1given(0.622046, -0.208601, 0.754682), (0.203541, 0.973801, 0.101399), (-0.756062, 0.090534, 0.648208)3.87737, -4.57359, 17.4522
2given(-0.218897, -0.262489, 0.939779), (0.253902, 0.914635, 0.314606), (-0.942135, 0.307478, -0.133565)20.049299, -6.79542, 25.4424
3given(-0.902384, -0.110257, 0.416589), (0.116992, 0.867727, 0.483076), (-0.414748, 0.484658, -0.770124)36.990898, -4.99859, 17.9256
4given(-0.899527, 0.113427, -0.421883), (-0.114995, 0.870172, 0.479142), (0.421459, 0.479515, -0.7697)41.499298, -0.117336, 0.70897
5given(-0.224164, 0.252464, -0.941282), (-0.256609, 0.916487, 0.306924), (0.940161, 0.310343, -0.140659)30.215, 3.7768, -13.33
6given(0.624853, 0.206334, -0.752984), (-0.20735, 0.973668, 0.09474), (0.752705, 0.096933, 0.651183)11.6802, 3.83705, -13.7234
7given(-0.147048, -0.628809, 0.763528), (-0.977666, 0.209578, -0.015689), (-0.150153, -0.748783, -0.645584)122.619003, 33.770401, -33.651199
8given(-0.011584, -0.999841, -0.013552), (-0.996446, 0.010411, 0.083589), (-0.083434, 0.014472, -0.996408)47.6451, 50.0742, -93.868301
9given(0.141332, -0.608613, -0.780779), (-0.980924, -0.192427, -0.027565), (-0.133466, 0.769781, -0.624199)-48.104698, 44.026199, -74.751099
10given(0.19199, 0.237896, -0.952127), (-0.939393, -0.236249, -0.248451), (-0.284044, 0.942121, 0.17812)-91.840302, 21.002701, 9.01318
11given(0.097412, 0.90289, -0.418689), (-0.900636, -0.099048, -0.423136), (-0.423516, 0.418305, 0.803527)-52.1422, -2.80113, 93.938698
12given(-0.078982, 0.893669, 0.441721), (-0.899929, 0.12669, -0.417226), (-0.428824, -0.430471, 0.794233)44.319302, -8.58076, 117.087997
13given(-0.181746, 0.20513, 0.961712), (-0.937353, 0.259462, -0.232485), (-0.297217, -0.943717, 0.145123)121.499001, 8.60645, 59.125
14given(0.587008, -0.219067, 0.779379), (0.24953, 0.964783, 0.083241), (-0.770167, 0.145616, 0.620999)5.98554, -7.09972, 18.663601
15given(-0.239541, -0.229775, 0.943305), (0.34487, 0.888092, 0.303902), (-0.907571, 0.398115, -0.133492)21.1278, -10.7143, 24.475
16given(-0.919718, -0.077227, 0.384908), (0.145179, 0.844046, 0.516245), (-0.364749, 0.530681, -0.765073)38.9389, -6.98361, 17.443199
17given(-0.870824, 0.111804, -0.478712), (-0.167289, 0.848278, 0.502432), (0.462256, 0.517613, -0.719998)43.306702, -1.23073, 0.712007
18given(-0.168006, 0.246852, -0.954378), (-0.310584, 0.905578, 0.288904), (0.935581, 0.344953, -0.075474)31.070999, 2.90082, -12.7028
19given(-0.178942, 0.163619, 0.970159), (-0.920832, 0.319408, -0.223713), (-0.34648, -0.933385, 0.09351)124.834, 5.00935, 56.389599
20given(-0.169981, -0.647586, 0.742791), (-0.958724, 0.283022, 0.02735), (-0.227938, -0.707482, -0.668964)122.692001, 33.3237, -34.129398
21given(-0.018693, -0.99786, -0.062665), (-0.991332, 0.010346, 0.130972), (-0.130043, 0.06457, -0.989404)44.330101, 53.3382, -91.918503
22given(0.140802, -0.562705, -0.814578), (-0.975032, -0.221524, -0.015509), (-0.171722, 0.796423, -0.579846)-50.959202, 44.891701, -68.067398
23given(0.07875, 0.904053, -0.420103), (-0.899189, -0.117531, -0.42148), (-0.430415, 0.410943, 0.803659)-51.4795, -1.97282, 94.372803
24given(-0.087868, 0.868991, 0.486964), (-0.889836, 0.151256, -0.430481), (-0.44774, -0.471143, 0.759969)51.9086, -12.0305, 116.628998
25given(0.082139, 0.901931, -0.423998), (-0.898461, -0.1171, -0.423149), (-0.431301, 0.415703, 0.800731)-52.119202, -2.50683, 93.888

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Components

#1: Protein
Hemolysin /


Mass: 65721.242 Da / Num. of mol.: 14 / Fragment: UNP residues 161-741
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae 12129(1) (bacteria) / Gene: VCG_000884 / Plasmid: PHIS-PARALLEL2 / Production host: Escherichia coli (E. coli) / Strain (production host): ORIGAMI B / References: UniProt: C2C744, UniProt: P09545*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 650 / 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: 3.75 Å3/Da / Density % sol: 67.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: 20 mM HEPES, 10% PEG 2000, 20 mM Cobalt(III) Hexammine Choride, 1 mM C10E8, pH 7.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSSRL BL12-211.25499, 1.25462, 1.03317
SYNCHROTRONSSRL BL12-221
Detector
TypeIDDetectorDate
MARMOSAIC 325 mm CCD1CCDJan 1, 2009
MARMOSAIC 325 mm CCD2CCDJan 1, 2009
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Liquid nitrogen-cooled double crystalMADMx-ray1
2Liquid nitrogen-cooled double crystalSINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.254991
21.254621
31.033171
411
ReflectionRedundancy: 6.7 % / Av σ(I) over netI: 14.02 / Number: 696052 / Rmerge(I) obs: 0.223 / Χ2: 1.21 / D res high: 4 Å / D res low: 100 Å / Num. obs: 104246 / % possible obs: 85.5
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
8.6210099.810.0951.4977.2
6.848.6210010.1651.1727.5
5.976.8410010.2941.0747.6
5.435.9710010.3361.1017.6
5.045.4310010.3591.1727.5
4.745.0499.610.41.2597.1
4.54.7483.310.4271.2635.8
4.314.566.910.5211.1615.2
4.144.3156.310.6381.1024.5
44.1447.210.8071.0773.5
ReflectionResolution: 2.88→100 Å / Num. obs: 299154 / % possible obs: 98.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.096 / Χ2: 0.996 / Net I/σ(I): 8.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.88-34.30.505288590.8391,296.3
3-3.124.60.406297830.871,299.3
3.12-3.274.60.295299070.9171,299.6
3.27-3.444.60.217299260.9891,299.7
3.44-3.654.60.154300161.0471,299.6
3.65-3.944.60.113300251.1431,299.6
3.94-4.334.60.076300411.1141,299.6
4.33-4.964.60.059301701.0651,299.4
4.96-6.254.60.055301360.9821,298.9
6.25-1004.50.035302910.9721,296.9

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
PHENIX1.5_2refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 2.88→43.956 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.35 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 13889 5.04 %Random
Rwork0.2176 ---
obs0.2192 275516 90.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 20 Å2 / ksol: 0.286 e/Å3
Displacement parametersBiso max: 140.87 Å2 / Biso mean: 55.2557 Å2 / Biso min: 11.65 Å2
Baniso -1Baniso -2Baniso -3
1-9.461 Å20 Å2-0 Å2
2--14.9775 Å2-0 Å2
3----24.4384 Å2
Refine analyzeLuzzati coordinate error obs: 0.4156 Å
Refinement stepCycle: LAST / Resolution: 2.88→43.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms62298 0 0 650 62948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00863650
X-RAY DIFFRACTIONf_angle_d1.05386684
X-RAY DIFFRACTIONf_chiral_restr0.0689579
X-RAY DIFFRACTIONf_plane_restr0.00411507
X-RAY DIFFRACTIONf_dihedral_angle_d17.07821736
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A3529X-RAY DIFFRACTIONPOSITIONAL0.054
12B3529X-RAY DIFFRACTIONPOSITIONAL0.054
13C3504X-RAY DIFFRACTIONPOSITIONAL0.055
14D3533X-RAY DIFFRACTIONPOSITIONAL0.056
15E3522X-RAY DIFFRACTIONPOSITIONAL0.051
16F3522X-RAY DIFFRACTIONPOSITIONAL0.054
17G3514X-RAY DIFFRACTIONPOSITIONAL0.055
18H3533X-RAY DIFFRACTIONPOSITIONAL0.057
19I3525X-RAY DIFFRACTIONPOSITIONAL0.051
110J3537X-RAY DIFFRACTIONPOSITIONAL0.055
111K3502X-RAY DIFFRACTIONPOSITIONAL0.059
112L3524X-RAY DIFFRACTIONPOSITIONAL0.046
113M3525X-RAY DIFFRACTIONPOSITIONAL0.048
114N3509X-RAY DIFFRACTIONPOSITIONAL0.058
21B911X-RAY DIFFRACTIONPOSITIONAL0.041
22C911X-RAY DIFFRACTIONPOSITIONAL0.041
23D911X-RAY DIFFRACTIONPOSITIONAL0.049
24E917X-RAY DIFFRACTIONPOSITIONAL0.045
25F877X-RAY DIFFRACTIONPOSITIONAL0.045
26G896X-RAY DIFFRACTIONPOSITIONAL0.045
27H914X-RAY DIFFRACTIONPOSITIONAL0.043
28I917X-RAY DIFFRACTIONPOSITIONAL0.049
29J917X-RAY DIFFRACTIONPOSITIONAL0.043
210K899X-RAY DIFFRACTIONPOSITIONAL0.045
211M911X-RAY DIFFRACTIONPOSITIONAL0.037
212N896X-RAY DIFFRACTIONPOSITIONAL0.044
31A915X-RAY DIFFRACTIONPOSITIONAL0.044
32L915X-RAY DIFFRACTIONPOSITIONAL0.044
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.88-2.92010.3413070.31616193650065
2.9201-2.95450.35123950.30017469786478
2.9545-2.99050.36744300.30577694812481
2.9905-3.02830.33784350.29467764819981
3.0283-3.06820.32694360.28847912834884
3.0682-3.11020.34364520.2788077852985
3.1102-3.15460.334570.28438135859285
3.1546-3.20170.31424300.27568264869487
3.2017-3.25170.31194380.26288401883988
3.2517-3.3050.29874530.26858532898589
3.305-3.36190.30874570.25898436889389
3.3619-3.42310.30484380.25288605904390
3.4231-3.48890.28744650.25138759922491
3.4889-3.56010.26534950.23518754924992
3.5601-3.63740.28074880.23548906939493
3.6374-3.7220.26854690.22798987945694
3.722-3.8150.26414960.21729012950894
3.815-3.91810.23064530.21399021947494
3.9181-4.03330.235040.19949109961395
4.0333-4.16340.23425100.19859114962495
4.1634-4.31210.2154550.18019280973596
4.3121-4.48460.19334830.17149339982297
4.4846-4.68850.1834920.16279357984997
4.6885-4.93540.18155110.15919372988397
4.9354-5.24410.17494930.15989444993798
5.2441-5.64820.21094530.17639474992798
5.6482-6.21520.21595090.18479465997497
6.2152-7.11130.2264870.199295321001997
7.1113-8.94710.2054840.178595981008297
8.9471-43.96090.21845140.220196221013695

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