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- PDB-6aqk: Crystal structure of the C-terminal toxin domain of RHS2 from Yer... -

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Basic information

Entry
Database: PDB / ID: 6aqk
TitleCrystal structure of the C-terminal toxin domain of RHS2 from Yersinia entomophaga
ComponentsToxin protein
KeywordsTOXIN / ADP-ribosylation / ADP-ribosyltransferase
Function / homologyToxin complex C-like repeat / Tripartite Tc toxins repeat / Rhs repeat-associated core / : / metal ion binding / BROMIDE ION / : / RHS2
Function and homology information
Biological speciesYersinia entomophaga (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.8 Å
AuthorsBusby, J.N. / Hurst, M.R.H. / Lott, J.S.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Marsden Fund14-UOA-146 New Zealand
CitationJournal: To be published
Title: Crystal structure of the C-terminal toxin domain of RHS2 from Yersinia entomophaga
Authors: Busby, J.N. / Hurst, M.R.H. / Lott, J.S.
History
DepositionAug 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toxin protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,63317
Polymers26,0631
Non-polymers1,56916
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.510, 54.520, 100.820
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Toxin protein


Mass: 26063.283 Da / Num. of mol.: 1 / Fragment: UNP residues 738-963
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia entomophaga (bacteria) / Gene: RHS2 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): LOBSTR(DE3) / References: UniProt: A0A2D0TC51*PLUS
#2: Chemical
ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Pt
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFirst 4 N-terminal residues GSGA are from a purification tag

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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: 1.98 Å3/Da / Density % sol: 37.81 % / Description: plate
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7.5 / Details: 29% PEG 2000 MME, 0.15 M KBr

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 1.07219 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 15, 2017
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07219 Å / Relative weight: 1
ReflectionResolution: 1.8→50.41 Å / Num. obs: 18821 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 13.523 % / Biso Wilson estimate: 42.029 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.111 / Χ2: 1.091 / Net I/σ(I): 11.92 / Num. measured all: 499693 / Scaling rejects: 398
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.859.6882.095125906273826740.3992.21297.7
1.85-1.912.0631.5771.5732183266826680.6171.647100
1.9-1.9513.9041.362.0536275260926090.7841.412100
1.95-2.0114.3680.9723.0436207252025200.8551.008100
2.01-2.0814.2610.7633.8234967245224520.9270.792100
2.08-2.1514.1050.5565.1633162235123510.9520.577100
2.15-2.2313.7280.4286.5530956225522550.9670.445100
2.23-2.3213.2230.3417.8129395222322230.9810.355100
2.32-2.4313.5480.289.528179208020800.9860.291100
2.43-2.5514.5090.22711.7329555203720370.9930.236100
2.55-2.6814.560.18914.0528043192619260.9920.196100
2.68-2.8514.3120.1517.0825561178617860.9940.156100
2.85-3.0413.9480.12720.0723823170817080.9960.132100
3.04-3.2913.0320.123.3320486157215720.9970.105100
3.29-3.613.410.08427.7119592146114610.9980.087100
3.6-4.0314.7060.07932.3119339131513150.9980.081100
4.03-4.6514.3720.07133.616873117411740.9980.074100
4.65-5.6913.8480.06433.23134609729720.9990.066100
5.69-8.0513.0270.06132.8197707507500.9980.064100
8.05-50.4114.2270.04636.959614204190.9990.04799.8

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Phasing

PhasingMethod: SAD
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 15837
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.42-100200.762504
5.04-6.4225.80.876501
4.38-5.0420.70.898505
3.96-4.3824.50.879505
3.66-3.9623.60.867505
3.43-3.6624.30.869502
3.25-3.4330.50.857511
3.1-3.25290.862515
2.98-3.131.10.841525
2.86-2.9832.70.819522
2.76-2.86310.829575
2.67-2.7630.40.846561
2.59-2.6733.80.82623
2.51-2.5931.40.836587
2.45-2.5134.40.822637
2.38-2.4530.10.842647
2.32-2.3830.20.847651
2.27-2.3232.90.828698
2.22-2.2731.50.829680
2.17-2.2231.90.819721
2.12-2.1734.20.818716
2.08-2.1232.10.806722
2.04-2.0834.20.792757
2.01-2.0432.40.784746
1.94-2.0136.50.751421

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
Blu-Icedata collection
XDSJun 1, 2017 BUILT=20170720data extraction
XSCALEJun 1, 2017 BUILT=20170720data scaling
Aimless0.5.32data reduction
SHELXDE2016/1phasing
DM7.0.044phasing
PDB_EXTRACT3.22data extraction
RefinementMethod to determine structure: SAD / Resolution: 1.8→50.41 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.233 / WRfactor Rwork: 0.181 / FOM work R set: 0.8024 / SU B: 3.682 / SU ML: 0.108 / SU R Cruickshank DPI: 0.1308 / SU Rfree: 0.1281 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.128 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 995 5 %RANDOM
Rwork0.181 ---
obs0.1834 18821 99.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 180.4 Å2 / Biso mean: 38.567 Å2 / Biso min: 24.51 Å2
Baniso -1Baniso -2Baniso -3
1--0.22 Å20 Å20 Å2
2---2 Å20 Å2
3---2.22 Å2
Refinement stepCycle: final / Resolution: 1.8→50.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1704 0 16 77 1797
Biso mean--74.76 40.93 -
Num. residues----216
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191758
X-RAY DIFFRACTIONr_bond_other_d0.0020.021542
X-RAY DIFFRACTIONr_angle_refined_deg1.8241.9452383
X-RAY DIFFRACTIONr_angle_other_deg1.0233598
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145217
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28624.56881
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47615292
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.54156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211964
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02358
LS refinement shellResolution: 1.8→1.847 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 67 -
Rwork0.303 1330 -
all-1397 -
obs--97.49 %

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