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- PDB-4igl: Structure of the RHS-repeat containing BC component of the secret... -

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Basic information

Entry
Database: PDB / ID: 4igl
TitleStructure of the RHS-repeat containing BC component of the secreted ABC toxin complex from Yersinia entomophaga
Components
  • YenB
  • YenC2
KeywordsTOXIN / Beta-Propeller / RHS / toxin complex / Toxin transporter/chaperone / Secreted
Function / homology
Function and homology information


: / extracellular region / cytoplasm
Similarity search - Function
YwqJ-like deaminase / YwqJ-like deaminase / Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein ...YwqJ-like deaminase / YwqJ-like deaminase / Shell / RHS repeat-associated core / RHS repeat-associated core / Insecticide toxin TcdB middle/C-terminal / Insecticide toxin TcdB middle/N-terminal / Insecticide toxin TcdB middle/C-terminal region / Insecticide toxin TcdB middle/N-terminal region / Salmonella virulence plasmid 65kDa B protein / Salmonella virulence plasmid 65kDa B protein / Toxin complex C-like repeat / Tripartite Tc toxins repeat / Rhs repeat-associated core / Regulator of chromosome condensation (RCC1) signature 2. / Integrin alpha, N-terminal / Mainly Beta
Similarity search - Domain/homology
: / Toxin subunit YenB / Toxin subunit YenC2
Similarity search - Component
Biological speciesYersinia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.49 Å
AuthorsBusby, J.N. / Panjikar, S. / Landsberg, M.J. / Hurst, M.R.H. / Lott, J.S.
CitationJournal: Nature / Year: 2013
Title: The BC component of ABC toxins is an RHS-repeat-containing protein encapsulation device
Authors: Busby, J.N. / Panjikar, S. / Landsberg, M.J. / Hurst, M.R.H. / Lott, J.S.
History
DepositionDec 17, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 7, 2013Provider: repository / Type: Initial release
Revision 1.1Oct 2, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: YenB
B: YenC2
C: YenB
D: YenC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)488,15318
Polymers487,1814
Non-polymers97114
Water44,4432467
1
A: YenB
B: YenC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)243,8927
Polymers243,5912
Non-polymers3015
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8810 Å2
ΔGint-37 kcal/mol
Surface area85040 Å2
MethodPISA
2
C: YenB
D: YenC2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)244,26011
Polymers243,5912
Non-polymers6709
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10180 Å2
ΔGint-37 kcal/mol
Surface area83930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)133.719, 147.596, 274.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein YenB


Mass: 167205.047 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Cloned into MCS1 / Source: (gene. exp.) Yersinia (bacteria) / Strain: MH-1 / Gene: yenB / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A880
#2: Protein YenC2


Mass: 76385.539 Da / Num. of mol.: 2 / Fragment: N-terminal domain, residues 1-690
Source method: isolated from a genetically manipulated source
Details: Cloned into MCS2 / Source: (gene. exp.) Yersinia (bacteria) / Strain: MH-1 / Gene: yenC2 / Plasmid: pETDuet-1 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2(DE3) / References: UniProt: B6A882
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2467 / 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: 2.78 Å3/Da / Density % sol: 55.73 % / Mosaicity: 0.22 °
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 18% PEG 3350, 150mM potassium phosphate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.953694 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 2, 2012
RadiationMonochromator: Double Si(111) with sagittaly bent second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953694 Å / Relative weight: 1
ReflectionResolution: 2.264→137.177 Å / Num. all: 245045 / Num. obs: 245045 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13.8 % / Biso Wilson estimate: 37.31 Å2 / Rmerge(I) obs: 0.3 / Rsym value: 0.3 / Net I/σ(I): 9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) all% possible all
2.26-2.33.32.6220.42203667091.52454.7
12.4-49.5512.80.03833.92172716980.01198.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation9.85 Å49.55 Å
Translation9.85 Å49.55 Å

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Processing

Software
NameVersionClassificationNB
Aimless0.1.27data scaling
PHASER2.5.2phasing
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Autobuilt model of non-isomorphous crystal solved by SeMet MAD

Resolution: 2.49→49.549 Å / Occupancy max: 1 / Occupancy min: 0.36 / FOM work R set: 0.8228 / SU ML: 0.31 / σ(F): 1.34 / Phase error: 25.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2506 9501 5.01 %
Rwork0.1999 --
obs0.2025 189671 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 101.94 Å2 / Biso mean: 48.6889 Å2 / Biso min: 28.24 Å2
Refinement stepCycle: LAST / Resolution: 2.49→49.549 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32974 0 54 2467 35495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00533873
X-RAY DIFFRACTIONf_angle_d0.93646190
X-RAY DIFFRACTIONf_chiral_restr0.0595039
X-RAY DIFFRACTIONf_plane_restr0.0046102
X-RAY DIFFRACTIONf_dihedral_angle_d13.31912156
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.49-2.51830.32692800.28859966276
2.5183-2.54790.36632970.298659436240
2.5479-2.5790.35773190.287459166235
2.579-2.61160.33423300.275359376267
2.6116-2.6460.33653070.271159596266
2.646-2.68220.32622960.258460056301
2.6822-2.72060.29073140.254959366250
2.7206-2.76120.32433370.268859216258
2.7612-2.80430.323000.255259876287
2.8043-2.85030.3443380.254359316269
2.8503-2.89940.30233080.243759686276
2.8994-2.95210.30333300.239659566286
2.9521-3.00890.29563490.22759076256
3.0089-3.07030.29863290.231559546283
3.0703-3.13710.28982820.21660246306
3.1371-3.210.27653150.217259906305
3.21-3.29030.27833250.213859726297
3.2903-3.37920.25663040.205759796283
3.3792-3.47870.24942970.199860106307
3.4787-3.59090.24932950.191260196314
3.5909-3.71920.23023170.182660396356
3.7192-3.86810.22053270.181959836310
3.8681-4.0440.21063220.178960096331
4.044-4.25710.21993180.170160106328
4.2571-4.52370.20833220.159960506372
4.5237-4.87270.20123350.154560266361
4.8727-5.36250.22253140.16861126426
5.3625-6.13720.22553280.173160956423
6.1372-7.72760.2113330.177961556488
7.7276-49.55850.18483330.166363816714

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