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- PDB-4g6v: CdiA-CT/CdiI toxin and immunity complex from Burkholderia pseudomallei -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 4g6v
TitleCdiA-CT/CdiI toxin and immunity complex from Burkholderia pseudomallei
Components
  • Adhesin/hemolysin
  • CdiI
KeywordsTOXIN / tRNase / immunity
Function / homology
Function and homology information


Alpha-Beta Plaits - #2920 / Trna Endonuclease; Chain: A, domain 1 - #120 / CDI inhibitor, Bp1026b-like / : / Trna Endonuclease; Chain: A, domain 1 / Alpha-Beta Plaits / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
BROMIDE ION / CdiI / :
Similarity search - Component
Biological speciesBurkholderia pseudomallei 1026a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.64 Å
AuthorsMorse, R.P. / Nikolakakis, K. / Willet, J. / Gerrick, E. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of toxicity and immunity in contact-dependent growth inhibition (CDI) systems.
Authors: Morse, R.P. / Nikolakakis, K.C. / Willett, J.L. / Gerrick, E. / Low, D.A. / Hayes, C.S. / Goulding, C.W.
History
DepositionJul 19, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adhesin/hemolysin
B: CdiI
C: Adhesin/hemolysin
D: CdiI
E: Adhesin/hemolysin
F: CdiI
G: Adhesin/hemolysin
H: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,44816
Polymers122,8098
Non-polymers6398
Water59433
1
A: Adhesin/hemolysin
B: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8624
Polymers30,7022
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2170 Å2
ΔGint-5 kcal/mol
Surface area10510 Å2
MethodPISA
2
C: Adhesin/hemolysin
D: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8624
Polymers30,7022
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-5 kcal/mol
Surface area10500 Å2
MethodPISA
3
E: Adhesin/hemolysin
F: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8624
Polymers30,7022
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2280 Å2
ΔGint-6 kcal/mol
Surface area10490 Å2
MethodPISA
4
G: Adhesin/hemolysin
H: CdiI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8624
Polymers30,7022
Non-polymers1602
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-6 kcal/mol
Surface area10510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.963, 173.654, 174.822
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain A and (resseq 168:299 )
211chain C and (resseq 168:299 )
112chain E and (resseq 168:299 )
212chain G and (resseq 168:299 )
113chain B and (resseq 2:104 )
213chain D and (resseq 2:104 )
114chain F and (resseq 2:102 )
214chain H and (resseq 2:102 )

NCS ensembles :
ID
1
2
3
4

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Components

#1: Protein
Adhesin/hemolysin


Mass: 18228.092 Da / Num. of mol.: 4 / Fragment: UNP residues 2948-3122
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1026a (bacteria)
Strain: 1026b / Gene: BP1026A_3896 / Production host: Escherichia coli (E. coli) / References: UniProt: I2KQ03
#2: Protein
CdiI


Mass: 12474.045 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Burkholderia pseudomallei 1026a (bacteria)
Strain: 1026b / Gene: cdiI / Production host: Escherichia coli (E. coli) / References: UniProt: H9T8H3
#3: Chemical
ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Br
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.35 Å3/Da / Density % sol: 47.61 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.49 M sodium phosphate monobasic, 0.96 M potassium phosphate dibasic, 10 mM triethylene glycol, 504 nM chymotrypsin, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2011
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.64→43.4 Å / Num. obs: 34071 / % possible obs: 99.47 % / Observed criterion σ(I): -3 / Redundancy: 29.6 %
Reflection shellResolution: 2.64→2.74 Å / Redundancy: 30.1 % / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.64→43.4 Å / SU ML: 0.76 / σ(F): 1.35 / Phase error: 27.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2452 1720 5.06 %RANDOM
Rwork0.2045 ---
obs0.2065 33975 99.47 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.767 Å2 / ksol: 0.306 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-40.7875 Å2-0 Å2-0 Å2
2---22.6511 Å2-0 Å2
3----18.1364 Å2
Refinement stepCycle: LAST / Resolution: 2.64→43.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6928 0 8 33 6969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017038
X-RAY DIFFRACTIONf_angle_d1.1869590
X-RAY DIFFRACTIONf_dihedral_angle_d13.3762532
X-RAY DIFFRACTIONf_chiral_restr0.0761157
X-RAY DIFFRACTIONf_plane_restr0.0051267
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A949X-RAY DIFFRACTIONPOSITIONAL
12C949X-RAY DIFFRACTIONPOSITIONAL0.026
21E949X-RAY DIFFRACTIONPOSITIONAL
22G949X-RAY DIFFRACTIONPOSITIONAL0.096
31B785X-RAY DIFFRACTIONPOSITIONAL
32D785X-RAY DIFFRACTIONPOSITIONAL0.025
41F781X-RAY DIFFRACTIONPOSITIONAL
42H781X-RAY DIFFRACTIONPOSITIONAL0.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.71350.32211500.26422567X-RAY DIFFRACTION96
2.7135-2.80110.32081480.2322664X-RAY DIFFRACTION100
2.8011-2.90120.24771540.23262660X-RAY DIFFRACTION100
2.9012-3.01730.30661310.23122682X-RAY DIFFRACTION100
3.0173-3.15460.30691300.23922694X-RAY DIFFRACTION100
3.1546-3.32080.24591400.23612680X-RAY DIFFRACTION100
3.3208-3.52880.28661390.22012694X-RAY DIFFRACTION100
3.5288-3.80110.2361680.18792661X-RAY DIFFRACTION100
3.8011-4.18340.20571550.16612681X-RAY DIFFRACTION100
4.1834-4.7880.181410.14932722X-RAY DIFFRACTION100
4.788-6.02990.21261320.19972746X-RAY DIFFRACTION100
6.0299-43.41940.24071320.20912804X-RAY DIFFRACTION99

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