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- PDB-3hvn: Crystal structure of cytotoxin protein suilysin from Streptococcu... -

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Basic information

Entry
Database: PDB / ID: 3hvn
TitleCrystal structure of cytotoxin protein suilysin from Streptococcus suis
ComponentsHemolysin
KeywordsTOXIN / beta-strand rich / elongated rod like / pore forming
Function / homology
Function and homology information


hemolysis in another organism / cholesterol binding / : / toxin activity / membrane => GO:0016020 / host cell plasma membrane / extracellular region
Similarity search - Function
Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin ...Carboxypeptidase Inhibitor; Chain A - #20 / Perfringolysin / HIV-1 Reverse Transcriptase; Chain A, domain 3 / Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain / Perfringolysin, domain 4 / Carboxypeptidase Inhibitor; Chain A / Thiol-activated cytolysin C-terminal / Thiol-activated cytolysin, C-terminal domain superfamily / Thiol-activated cytolysin beta sandwich domain / Thiol-activated cytolysin / Thiol-activated cytolysin superfamily / Thiol-activated cytolysin, alpha-beta domain superfamily / Thiol-activated cytolysin / Glutaredoxin / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,1,1,3,3,3-hexafluoropropan-2-ol / HEPTANE-1,2,3-TRIOL / Thiol-activated cytolysin / Thiol-activated cytolysin
Similarity search - Component
Biological speciesStreptococcus suis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.852 Å
AuthorsXu, L. / Huang, B. / Du, H. / Zhang, C.X. / Xu, J. / Li, X. / Rao, Z.
CitationJournal: Protein Cell / Year: 2010
Title: Crystal structure of cytotoxin protein suilysin from Streptococcus suis.
Authors: Xu, L. / Huang, B. / Du, H. / Zhang, X.C. / Xu, J. / Li, X. / Rao, Z.
History
DepositionJun 16, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 1, 2020Group: Database references / Category: citation / citation_author / struct_ref_seq_dif
Item: _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed ..._citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _struct_ref_seq_dif.details
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hemolysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4173
Polymers56,1011
Non-polymers3162
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)95.720, 95.720, 117.046
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Hemolysin / / Suilysin


Mass: 56101.219 Da / Num. of mol.: 1 / Mutation: P353L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus suis (bacteria) / Strain: 05ZYH33 / Gene: sly / Plasmid: pGEX 6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q55996, UniProt: A4VW80*PLUS
#2: Chemical ChemComp-CFH / 1,1,1,3,3,3-hexafluoropropan-2-ol / Hexafluoro-2-propanol


Mass: 168.038 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H2F6O
#3: Chemical ChemComp-HTO / HEPTANE-1,2,3-TRIOL


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsHTO IS 1,2,3-HEPTANETRIOL ISOMER H.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)Mosaicity (°)
12.7655.420.411
2
Crystal growTemperature: 289 K / pH: 7
Details: 8% polyethylene glycol (PEG)3350, 0.12M sodium citrate (pH7.0), 5% 1,2,3-heptanetriol isomer H, 2% 1,1,1,3,3,3-hexafluoro-2-propanol, temperature 289K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11701
21702
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-5A11
SYNCHROTRONPhoton Factory BL-17A20.97866, 0.97934, 0.96410
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDOct 27, 2008
ADSC QUANTUM 2702CCDDec 1, 2008
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.978661
30.979341
40.96411
ReflectionRedundancy: 9.5 % / Av σ(I) over netI: 30.36 / Number: 122778 / Rmerge(I) obs: 0.082 / Χ2: 2.33 / D res high: 3 Å / D res low: 50 Å / Num. obs: 12949 / % possible obs: 98.2
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.46509710.0687.9727.7
5.136.4610010.0714.1129.9
4.485.1399.710.072.99910.3
4.074.4899.910.0722.07610.5
3.784.0710010.0941.5110.8
3.563.7810010.1261.4459.8
3.383.5610010.1611.03610.9
3.233.3810010.2210.88310.1
3.113.2398.710.30.7438.3
33.1186.610.3220.7746.2
ReflectionResolution: 2.85→50 Å / Num. obs: 13204 / % possible obs: 88.5 % / Redundancy: 5.7 % / Rmerge(I) obs: 0.052 / Χ2: 1.033 / Net I/σ(I): 30.364
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.85-2.955.60.3169680.86466.4
2.95-3.075.80.23312340.92683.7
3.07-3.215.80.17113181.02690.8
3.21-3.385.70.10713961.18694.3
3.38-3.595.80.07513751.1593.9
3.59-3.875.70.06314001.02193.8
3.87-4.265.70.05213770.98593.5
4.26-4.875.80.04414001.10992.4
4.87-6.145.80.04113581.06290.2
6.14-505.60.04313780.93185.5

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVEphasing
PHENIXrefinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.852→28.409 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.74 / σ(F): 0.16 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.294 637 5.03 %
Rwork0.279 --
obs0.28 12653 85.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 91.358 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso max: 291.42 Å2 / Biso mean: 131.101 Å2 / Biso min: 31.69 Å2
Baniso -1Baniso -2Baniso -3
1-11.282 Å20 Å2-0 Å2
2--11.282 Å20 Å2
3----36.063 Å2
Refinement stepCycle: LAST / Resolution: 2.852→28.409 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3648 0 20 7 3675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023942
X-RAY DIFFRACTIONf_angle_d0.4755095
X-RAY DIFFRACTIONf_chiral_restr0.033579
X-RAY DIFFRACTIONf_plane_restr0.002659
X-RAY DIFFRACTIONf_dihedral_angle_d12.4251330
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.852-3.0720.4561040.3951818192266
3.072-3.3810.361220.3492423254587
3.381-3.8690.3151530.3012568272192
3.869-4.8710.2491330.2492616274992
4.871-28.410.261250.2482591271688
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)
1-0.1165-1.23950.3640.09160.06840.2345-0.3704-0.16620.2677-0.15030.3026-0.1468-0.5173-0.14810.00010.6120.2775-0.0950.92250.09750.618323.013432.587332.234
20.5550.5689-0.54510.72730.58283.9984-0.1246-0.1218-0.00190.0253-0.2298-0.0744-0.3116-1.039-0.13760.22910.23710.04141.0957-0.16990.55286.026626.03636.4943
3-0.2212-0.1971-0.7916-0.84981.27772.1017-0.28190.05620.15040.3414-0.28620.09830.2098-0.381-00.71570.14740.1120.79740.06920.590615.710719.57444.2571
4-0.6957-0.3953-2.05653.8224-0.31555.58610.230.25450.0422-0.09440.12130.18310.8653-0.23851.66670.3706-0.07150.01530.3596-0.06770.385766.09997.497549.1041
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain A, 32-94A32 - 94
2X-RAY DIFFRACTION2chain A, 95-291A95 - 291
3X-RAY DIFFRACTION3chain A, 292-383A292 - 383
4X-RAY DIFFRACTION4chain A, 384-499A384 - 499

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