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- PDB-4bwg: Structural basis of subtilase cytotoxin SubAB assembly -

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Basic information

Entry
Database: PDB / ID: 4bwg
TitleStructural basis of subtilase cytotoxin SubAB assembly
Components
  • SUBA
  • SUBTILASE CYTOTOXIN, SUBUNIT B
KeywordsTOXIN / AB5 TOXINS / DISASSEMBLY / CELLULAR TRAFFICKING
Function / homology
Function and homology information


host cell endoplasmic reticulum lumen / host cell cytosol / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / toxin activity / serine-type endopeptidase activity / proteolysis / extracellular space / identical protein binding
Similarity search - Function
OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Endoplasmic reticulum targeting sequence. / Enterotoxin / Peptidase S8/S53 domain / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel ...OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Endoplasmic reticulum targeting sequence. / Enterotoxin / Peptidase S8/S53 domain / Serine proteases, subtilase domain profile. / Peptidase S8/S53 domain superfamily / Subtilase family / Peptidase S8/S53 domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Subtilase SubB / Subtilase cytotoxin subunit A
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLe Nours, J. / Paton, A.W. / Byres, E. / Troy, S. / Herdman, B.P. / Johnson, M.D. / Paton, J.C. / Rossjohn, J. / Beddoe, T.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Basis of Subtilase Cytotoxin Subab Assembly.
Authors: Le Nours, J. / Paton, A.W. / Byres, E. / Troy, S. / Herdman, B.P. / Johnson, M.D. / Paton, J.C. / Rossjohn, J. / Beddoe, T.
History
DepositionJul 2, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 21, 2013Group: Database references
Revision 1.2Oct 9, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SUBA
B: SUBTILASE CYTOTOXIN, SUBUNIT B
C: SUBTILASE CYTOTOXIN, SUBUNIT B
D: SUBTILASE CYTOTOXIN, SUBUNIT B
E: SUBTILASE CYTOTOXIN, SUBUNIT B
F: SUBTILASE CYTOTOXIN, SUBUNIT B
G: SUBA
H: SUBTILASE CYTOTOXIN, SUBUNIT B
I: SUBTILASE CYTOTOXIN, SUBUNIT B
J: SUBTILASE CYTOTOXIN, SUBUNIT B
K: SUBTILASE CYTOTOXIN, SUBUNIT B
L: SUBTILASE CYTOTOXIN, SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)207,30714
Polymers207,11912
Non-polymers1882
Water1,51384
1
A: SUBA
B: SUBTILASE CYTOTOXIN, SUBUNIT B
C: SUBTILASE CYTOTOXIN, SUBUNIT B
D: SUBTILASE CYTOTOXIN, SUBUNIT B
E: SUBTILASE CYTOTOXIN, SUBUNIT B
F: SUBTILASE CYTOTOXIN, SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6527
Polymers103,5596
Non-polymers921
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13110 Å2
ΔGint-57.8 kcal/mol
Surface area28780 Å2
MethodPISA
2
G: SUBA
H: SUBTILASE CYTOTOXIN, SUBUNIT B
I: SUBTILASE CYTOTOXIN, SUBUNIT B
J: SUBTILASE CYTOTOXIN, SUBUNIT B
K: SUBTILASE CYTOTOXIN, SUBUNIT B
L: SUBTILASE CYTOTOXIN, SUBUNIT B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,6567
Polymers103,5596
Non-polymers961
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12310 Å2
ΔGint-69.5 kcal/mol
Surface area28880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.212, 81.712, 227.791
Angle α, β, γ (deg.)90.00, 100.24, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SUBA


Mass: 37535.898 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: 98NK2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q6EZC2
#2: Protein
SUBTILASE CYTOTOXIN, SUBUNIT B / SUBB


Mass: 13204.717 Da / Num. of mol.: 10 / Fragment: RESIDUES 24-141
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: 98NK2 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q3ZTX8
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.7 Å3/Da / Density % sol: 54.6 % / Description: NONE
Crystal growpH: 3.1 / Details: 11% PEG8K, 0.5M LISO4, 0.1M CITRATE PH 3.1

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 0.94
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 2.6→66.08 Å / Num. obs: 252165 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 48.79 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 11.3
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.3 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTIES 3DWA AND 2IY9

3dwa

2iy9


Resolution: 2.6→38.07 Å / Cor.coef. Fo:Fc: 0.8957 / Cor.coef. Fo:Fc free: 0.8621 / SU R Cruickshank DPI: 0.511 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.468 / SU Rfree Blow DPI: 0.273 / SU Rfree Cruickshank DPI: 0.283
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2496 3347 5.06 %RANDOM
Rwork0.2192 ---
obs0.2207 66102 99.93 %-
Displacement parametersBiso mean: 55.91 Å2
Baniso -1Baniso -2Baniso -3
1--0.756 Å20 Å21.8146 Å2
2---4.9733 Å20 Å2
3---5.7293 Å2
Refine analyzeLuzzati coordinate error obs: 0.527 Å
Refinement stepCycle: LAST / Resolution: 2.6→38.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12419 0 11 84 12514
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0112895HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0917659HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5502SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes219HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1950HARMONIC5
X-RAY DIFFRACTIONt_it12895HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.58
X-RAY DIFFRACTIONt_other_torsion2.65
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1778SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14898SEMIHARMONIC4
LS refinement shellResolution: 2.6→2.67 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2561 257 5.29 %
Rwork0.2327 4601 -
all0.234 4858 -
obs--99.93 %
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)
12.1268-1.6845-1.17285.24673.213.14170.11860.0989-0.4108-0.8919-0.55660.945-0.7479-0.33240.4379-0.04880.0781-0.2034-0.2709-0.0864-0.0586-8.900713.45233.9888
21.16881.3047-1.91924.47810.54782.3723-0.2471-0.0805-0.6820.4596-0.50041.18910.7591-0.28710.7475-0.1635-0.0840.1646-0.5029-0.22070.6926-7.0798-28.303528.9858
33.4031-2.6275-1.93438.10642.94924.8298-0.0489-0.25370.1012-0.58050.7185-1.211-0.14860.8785-0.6696-0.2505-0.05970.0892-0.0694-0.19940.096221.3741-5.606928.4295
41.23022.33061.54376.58054.90657.9154-0.05230.2954-0.7833-1.2156-0.53710.6676-0.4248-0.83680.5894-0.130.0876-0.4182-0.3918-0.29310.3718-7.8041-18.48518.9663
53.2931-0.685-0.07101.20192.5160.38060.2815-0.1236-1.1245-0.22950.1016-0.54710.0296-0.15110.62560.06280.0452-0.5677-0.0868-0.432710.9946-3.98617.832
61.1140.9848-0.35115.45470.58152.4843-0.408-0.4543-0.53751.06980.31050.20121.00840.73790.09750.17680.24750.2374-0.2860.13710.0539.8444-21.21140.1886
74.10320.8783-3.34861.4112-1.49287.40950.2126-0.68950.1317-0.0553-0.1966-0.0472-0.26150.9815-0.016-0.2383-0.06240.0526-0.0641-0.0627-0.241922.073930.129260.9136
83.6503-0.97243.47933.2230.94042.377-0.11120.1006-0.14780.81570.19440.11160.68310.6557-0.0832-0.150.23430.10050.60790.1472-0.430520.201218.0201102.1094
96.23920.7268-6.81362.7299-2.12099.45230.27560.25620.3920.04830.24420.2299-0.729-1.0598-0.5197-0.32750.08120.04620.26830.0023-0.2667-8.527927.923381.182
100.1614-2.21991.26162.70583.53354.7691-0.0758-0.70770.13790.30720.2965-0.4674-0.4456-0.0844-0.2207-0.1431-0.26760.04010.3783-0.2284-0.313820.301139.1768100.7265
112.53981.13642.95913.02125.52670.98620.09-0.3420.64420.3636-0.1040.1168-1.0893-0.13790.0140.4667-0.04520.4778-0.39-0.1642-0.35453.852947.13487.6075
120.5032-0.09592.41572.4663-0.10862.2245-0.2646-0.5519-0.49050.2504-0.07730.3690.99840.00170.34190.1540.06480.34270.1510.2387-0.15032.344810.707290.5156
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H
9X-RAY DIFFRACTION9CHAIN I
10X-RAY DIFFRACTION10CHAIN J
11X-RAY DIFFRACTION11CHAIN K
12X-RAY DIFFRACTION12CHAIN L

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