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- PDB-6v9p: Crystal structure of the transposition protein TniQ -

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Basic information

Entry
Database: PDB / ID: 6v9p
TitleCrystal structure of the transposition protein TniQ
ComponentsTniQ family protein
KeywordsIMMUNE SYSTEM / Type I-F CRISPR-Cas system / transposition / TniQ
Function / homology:
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsJia, N. / Patel, D.J.
CitationJournal: Cell Res / Year: 2020
Title: Structure-function insights into the initial step of DNA integration by a CRISPR-Cas-Transposon complex.
Authors: Ning Jia / Wei Xie / M Jason de la Cruz / Edward T Eng / Dinshaw J Patel /
History
DepositionDec 14, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Mar 6, 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: TniQ family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9084
Polymers45,6851
Non-polymers2233
Water99155
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: TniQ family protein
hetero molecules

A: TniQ family protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,8168
Polymers91,3702
Non-polymers4466
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Buried area4250 Å2
ΔGint-14 kcal/mol
Surface area31710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.822, 69.822, 179.491
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein TniQ family protein


Mass: 45684.945 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: FXE93_08745 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A5C9LJ33
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2% PEG 6K, 0.1 Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.93→65.07 Å / Num. obs: 34495 / % possible obs: 99.9 % / Redundancy: 24.4 % / Biso Wilson estimate: 47.49 Å2 / CC1/2: 1 / Net I/σ(I): 34.7
Reflection shellResolution: 1.93→1.97 Å / Num. unique obs: 2240 / CC1/2: 0.78

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
XDSdata reduction
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→65.07 Å / SU ML: 0.2992 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.9723
RfactorNum. reflection% reflection
Rfree0.2615 1992 5.82 %
Rwork0.2278 --
obs0.2298 34243 99.4 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 59.66 Å2
Refinement stepCycle: LAST / Resolution: 1.93→65.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3050 0 8 55 3113
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00733153
X-RAY DIFFRACTIONf_angle_d0.94564267
X-RAY DIFFRACTIONf_chiral_restr0.0511453
X-RAY DIFFRACTIONf_plane_restr0.008547
X-RAY DIFFRACTIONf_dihedral_angle_d11.53961860
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-1.980.4541370.39192214X-RAY DIFFRACTION97.47
1.98-2.030.42221370.34642240X-RAY DIFFRACTION99.17
2.03-2.090.35081410.29392245X-RAY DIFFRACTION98.68
2.09-2.160.33891390.28462257X-RAY DIFFRACTION99.54
2.16-2.230.30451390.27182263X-RAY DIFFRACTION99.38
2.23-2.320.31591410.27242277X-RAY DIFFRACTION99.22
2.32-2.430.3411390.25752259X-RAY DIFFRACTION99.34
2.43-2.560.29521410.27562283X-RAY DIFFRACTION99.51
2.56-2.720.32161400.26352282X-RAY DIFFRACTION99.63
2.72-2.930.33521450.26112333X-RAY DIFFRACTION99.76
2.93-3.220.29181440.26582316X-RAY DIFFRACTION99.88
3.22-3.690.271450.22992356X-RAY DIFFRACTION100
3.69-4.650.2231480.19552384X-RAY DIFFRACTION99.96
4.65-65.070.2121560.19232542X-RAY DIFFRACTION99.96

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