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- PDB-4c18: The structure of the Tsi2 dimer with a disulfide bond -

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Basic information

Entry
Database: PDB / ID: 4c18
TitleThe structure of the Tsi2 dimer with a disulfide bond
ComponentsTSI2
KeywordsTOXIN / IMMUNITY PROTEIN / T6SS / ANTI-TOXIN
Function / homologyHelix Hairpins - #2500 / Tse2 immunity protein Tsi2 / : / : / T6SS, Immune protein Tsi2-like / Helix Hairpins / Orthogonal Bundle / Mainly Alpha / Immune protein Tsi2
Function and homology information
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.49 Å
AuthorsRobb, C.S. / Nano, F.E. / Boraston, A.B.
CitationJournal: To be Published
Title: The Structure of Tse2 in Complex with Tsi2
Authors: Robb, C.S. / Cid, M. / Nano, F.E. / Boraston, A.B.
History
DepositionAug 10, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TSI2
B: TSI2


Theoretical massNumber of molelcules
Total (without water)21,6542
Polymers21,6542
Non-polymers00
Water1,58588
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-18.2 kcal/mol
Surface area9140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.970, 36.300, 37.860
Angle α, β, γ (deg.)107.37, 95.23, 92.11
Int Tables number1
Space group name H-MP1

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Components

#1: Protein TSI2


Mass: 10827.030 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9I0D9
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.17 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growDetails: 0.1M SODIUM CITRATE PH 5.6, 35% T-BUTANOL

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 11, 2011 / Details: RH COATED FLAT MIRROR, TOROIDAL FOCUSING MIRROR
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.49→35.93 Å / Num. obs: 21050 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 7.3
Reflection shellResolution: 1.49→1.57 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.7 / % possible all: 88.6

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3VPV

3vpv


Resolution: 1.49→34.59 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.926 / SU B: 2.068 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.1 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25886 1076 5.1 %RANDOM
Rwork0.22262 ---
obs0.22445 19974 91.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.916 Å2
Baniso -1Baniso -2Baniso -3
1--1.55 Å20.49 Å20.52 Å2
2---1.61 Å21.39 Å2
3---2.16 Å2
Refinement stepCycle: LAST / Resolution: 1.49→34.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 88 1236
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.021170
X-RAY DIFFRACTIONr_bond_other_d0.0060.021118
X-RAY DIFFRACTIONr_angle_refined_deg1.81221595
X-RAY DIFFRACTIONr_angle_other_deg1.3533.0022561
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5635151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.81826.89758
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.50215195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.889155
X-RAY DIFFRACTIONr_chiral_restr0.1150.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211376
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02241
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.494→1.533 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 90 -
Rwork0.27 1379 -
obs--86.41 %

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