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- PDB-1s3r: Crystal structure of the human-specific toxin intermedilysin -

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Basic information

Entry
Database: PDB / ID: 1s3r
TitleCrystal structure of the human-specific toxin intermedilysin
Componentsintermedilysin
KeywordsTOXIN
Function / homology
Function and homology information


cholesterol binding / toxin activity / killing of cells of another organism / host cell plasma membrane / extracellular region / membrane / metal ion binding
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
Thiol-activated cytolysin
Similarity search - Component
Biological speciesStreptococcus intermedius (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsPolekhina, G. / Giddings, K.S. / Tweten, R.K. / Parker, M.W.
Citation
Journal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Insights into the action of the superfamily of cholesterol-dependent cytolysins from studies of intermedilysin
Authors: Polekhina, G. / Giddings, K.S. / Tweten, R.K. / Parker, M.W.
#1: Journal: To be Published
Title: Crystallization and preliminary X-ray analysis of the human-specific toxin intermedilysin
Authors: Polekhina, G. / Giddings, K.S. / Tweten, R.K. / Parker, M.W.
#2: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003
Title: Redefining cholesterol's role in the mechanism of the cholesterol-dependent cytolysins
Authors: Giddings, K.S. / Johnson, A.E. / Tweten, R.K.
History
DepositionJan 14, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: intermedilysin
B: intermedilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,5146
Polymers118,1302
Non-polymers3844
Water8,125451
1
A: intermedilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2573
Polymers59,0651
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: intermedilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,2573
Polymers59,0651
Non-polymers1922
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2560 Å2
ΔGint-72 kcal/mol
Surface area45630 Å2
MethodPISA
4
A: intermedilysin
B: intermedilysin
hetero molecules

A: intermedilysin
B: intermedilysin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)237,02812
Polymers236,2604
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
MethodPQS
Unit cell
Length a, b, c (Å)88.450, 173.640, 105.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERASPASPAA57 - 7460 - 77
21SERSERASPASPBB57 - 7460 - 77
12VALVALVALVALAA103 - 324106 - 327
22VALVALVALVALBB103 - 324106 - 327
13ALAALATHRTHRAA380 - 414383 - 417
23ALAALATHRTHRBB380 - 414383 - 417
14ASPASPGLYGLYAA418 - 441421 - 444
24ASPASPGLYGLYBB418 - 441421 - 444
15ILEILEGLYGLYAA450 - 485453 - 488
25ILEILEGLYGLYBB450 - 485453 - 488
16ILEILELYSLYSAA497 - 528500 - 531
26ILEILELYSLYSBB497 - 528500 - 531

NCS ensembles :
ID
1
2
3
4
5
6
Detailsmonomer, two molecules present in asymmetric unit related by 2-fold non-crystallographic symmetry

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Components

#1: Protein intermedilysin


Mass: 59064.875 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus intermedius (bacteria) / Plasmid: pTrcHisA / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LCB8
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 451 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.68 Å3/Da / Density % sol: 66.34 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 8000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineTypeIDWavelength (Å)
SYNCHROTRONAPS 14-BM-C10.9
ROTATING ANODERIGAKU21.54
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 41CCDJul 14, 2002
MARRESEARCH2IMAGE PLATEApr 23, 2002mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
21.541
ReflectionResolution: 2.5→30 Å / Num. all: 50420 / Num. obs: 50420 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 81.7 Å2 / Rmerge(I) obs: 0.047 / Rsym value: 0.047 / Net I/σ(I): 37.7
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 6 % / Rmerge(I) obs: 0.368 / Mean I/σ(I) obs: 4.5 / Rsym value: 0.368 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→30 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.911 / SU B: 14.688 / SU ML: 0.292 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.417 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2951 2570 5.1 %RANDOM
Rwork0.22901 ---
all0.265 50420 --
obs0.23233 47850 99.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 35.356 Å2
Baniso -1Baniso -2Baniso -3
1-12.99 Å20 Å20 Å2
2---9.54 Å20 Å2
3----3.45 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7356 0 20 451 7827
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0217528
X-RAY DIFFRACTIONr_bond_other_d0.0020.026676
X-RAY DIFFRACTIONr_angle_refined_deg1.5821.94210220
X-RAY DIFFRACTIONr_angle_other_deg0.905315620
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1135944
X-RAY DIFFRACTIONr_chiral_restr0.090.21150
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028374
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021464
X-RAY DIFFRACTIONr_nbd_refined0.230.21705
X-RAY DIFFRACTIONr_nbd_other0.2510.28116
X-RAY DIFFRACTIONr_nbtor_other0.0910.24612
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.190.2309
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1340.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.257
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2270.28
X-RAY DIFFRACTIONr_mcbond_it0.7211.54706
X-RAY DIFFRACTIONr_mcangle_it1.30127618
X-RAY DIFFRACTIONr_scbond_it1.84432822
X-RAY DIFFRACTIONr_scangle_it2.9434.52602
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
1272medium positional0.160.5
23236medium positional0.180.5
3503medium positional0.180.5
4363medium positional0.150.5
5565medium positional0.150.5
6506medium positional0.170.5
1272medium thermal0.772
23236medium thermal1.352
3503medium thermal1.652
4363medium thermal0.972
5565medium thermal1.022
6506medium thermal0.512
LS refinement shellResolution: 2.59→2.69 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.554 166 -
Rwork0.464 3484 -
obs-5490 99.6 %
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)
11.3931-0.5925-0.07413.82090.35931.8011-0.163-0.1120.2590.8810.189-0.360.3620.026-0.0260.6029-0.035-0.15830.6132-0.09390.51919.8237.86840.295
21.17681.4984-0.29534.7805-1.54865.85310.482-0.391-0.0670.6710.2410.916-0.438-1.226-0.7231.01390.1447-0.29680.96990.29210.855611.706-14.97452.526
30.84590.00140.34533.78231.07323.285-0.0940.076-0.055-0.4190.1-0.351-0.5330.139-0.0060.27420.0006-0.01370.6532-0.08240.57720.064-28.89412.279
41.4247-1.41481.48196.5301-1.97676.50870.2180.249-0.1090.0260.3111.1030.294-1.042-0.5290.4279-0.1440.10150.85550.17250.72199.60226.1242.225
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA56 - 41659 - 419
2X-RAY DIFFRACTION2AA417 - 528420 - 531
3X-RAY DIFFRACTION3BB56 - 41659 - 419
4X-RAY DIFFRACTION4BB417 - 528420 - 531

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