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- PDB-4hz9: Crystal structure of the type VI native effector-immunity complex... -

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Basic information

Entry
Database: PDB / ID: 4hz9
TitleCrystal structure of the type VI native effector-immunity complex Tae3-Tai3 from Ralstonia pickettii
Components
  • Putative cytoplasmic protein
  • Putative periplasmic protein
KeywordsHYDROLASE / protein-protein complex / endopeptidase / periplasmic space
Function / homology
Function and homology information


Domain of unknown function DUF3828 / Protein of unknown function (DUF3828) / endopeptidase domain like (from Nostoc punctiforme) / endopeptidase fold (from Nostoc punctiforme) / Nuclear Transport Factor 2; Chain: A, - #50 / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Putative cytoplasmic protein / Putative periplasmic protein
Similarity search - Component
Biological speciesRalstonia pickettii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsDong, C. / Zhang, H. / Gao, Z.Q. / Dong, Y.H.
CitationJournal: Biochem.J. / Year: 2013
Title: Structural insights into the inhibition of type VI effector Tae3 by its immunity protein Tai3
Authors: Dong, C. / Zhang, H. / Gao, Z.Q. / Wang, W.J. / She, Z. / Liu, G.F. / Shen, Y.Q. / Su, X.D. / Dong, Y.H.
History
DepositionNov 14, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)47,4433
Polymers47,4433
Non-polymers00
Water2,072115
1
A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein

A: Putative cytoplasmic protein
B: Putative periplasmic protein
C: Putative periplasmic protein


Theoretical massNumber of molelcules
Total (without water)94,8866
Polymers94,8866
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area12950 Å2
ΔGint-28 kcal/mol
Surface area30100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.166, 144.382, 129.908
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Putative cytoplasmic protein / toxin protein


Mass: 13100.807 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3260 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF2
#2: Protein Putative periplasmic protein / antitoxin protein


Mass: 17171.004 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ralstonia pickettii (bacteria) / Strain: 12D / Gene: Rpic12D_3261 / Production host: Escherichia coli (E. coli) / References: UniProt: C6BHF3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.78 Å3/Da / Density % sol: 55.69 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.01M ferric chloride hexahydrate, 0.1M tri-sodium citrate dihydrate pH5.6, 10% v/v jeffamine M-600, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 0.9793 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 10, 2012
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 20876 / Num. obs: 20842 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7 % / Biso Wilson estimate: 35.03 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 18.4
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 5 % / Rmerge(I) obs: 0.532 / Mean I/σ(I) obs: 2 / % possible all: 90.4

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Processing

Software
NameVersionClassification
MAR345data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HZB

4hzb


Resolution: 2.4→48.286 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.38 / σ(F): 1.34 / Phase error: 22.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2317 1069 5.13 %
Rwork0.1912 --
obs0.1933 20842 98.83 %
all-20876 -
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 26.889 Å2 / ksol: 0.353 e/Å3
Displacement parametersBiso max: 117.98 Å2 / Biso mean: 36.3322 Å2 / Biso min: 9.15 Å2
Baniso -1Baniso -2Baniso -3
1-5.8127 Å2-0 Å2-0 Å2
2---4.3926 Å2-0 Å2
3----1.4201 Å2
Refinement stepCycle: LAST / Resolution: 2.4→48.286 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2918 0 0 115 3033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073010
X-RAY DIFFRACTIONf_angle_d1.0224107
X-RAY DIFFRACTIONf_dihedral_angle_d13.1821070
X-RAY DIFFRACTIONf_chiral_restr0.073427
X-RAY DIFFRACTIONf_plane_restr0.005534
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4004-2.50960.41651260.3392266239293
2.5096-2.64190.33631370.24642408254598
2.6419-2.80740.26421290.200624822611100
2.8074-3.02420.24151230.190224812604100
3.0242-3.32840.27611270.200425002627100
3.3284-3.80990.23871390.19625002639100
3.8099-4.79940.16871580.14624982656100
4.7994-48.29560.19791300.177526382768100
Refinement TLS params.Method: refined / Origin x: 5.2936 Å / Origin y: 15.5327 Å / Origin z: -0.0079 Å
111213212223313233
T0.0998 Å20.0222 Å2-0.0064 Å2-0.0842 Å20.0174 Å2--0.1192 Å2
L0.7266 °2-0.0042 °2-0.0095 °2-1.2267 °2-0.0519 °2--1.3558 °2
S-0.0179 Å °0.0246 Å °0.1796 Å °-0.042 Å °-0.0717 Å °-0.0304 Å °-0.3034 Å °-0.0497 Å °0.0587 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 119
2X-RAY DIFFRACTION1allB29 - 151
3X-RAY DIFFRACTION1allC30 - 151
4X-RAY DIFFRACTION1allA201 - 241
5X-RAY DIFFRACTION1allB201 - 247
6X-RAY DIFFRACTION1allC201 - 227

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