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- PDB-6lnd: Crystal structure of transposition protein TniQ -

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Basic information

Entry
Database: PDB / ID: 6lnd
TitleCrystal structure of transposition protein TniQ
Componentstransposition protein TniQ
KeywordsDNA BINDING PROTEIN / Type I-F CRISPR-Cas system: Csy Cascade: Structure: Tn7-like transposons: RNA-guided transition: transposase subunit
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 Å
AuthorsWang, B. / Xu, W. / Yang, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971135) China
CitationJournal: Cell Res / Year: 2020
Title: Structural basis of a Tn7-like transposase recruitment and DNA loading to CRISPR-Cas surveillance complex.
Authors: Beibei Wang / Wenhao Xu / Hui Yang /
History
DepositionDec 28, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
K: transposition protein TniQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,1543
Polymers46,0231
Non-polymers1312
Water1,820101
1
K: transposition protein TniQ
hetero molecules

K: transposition protein TniQ
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,3086
Polymers92,0472
Non-polymers2624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3840 Å2
ΔGint-13 kcal/mol
Surface area33520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.277, 66.277, 178.584
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein transposition protein TniQ


Mass: 46023.363 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Plasmid: pRSFDuet-SUMO / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.14 Å3/Da / Density % sol: 42.62 % / Mosaicity: 0.579 °
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.7
Details: 0.1 M Tris-HCl (pH 8.7), 2% Polyethylene glycol 8000 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 11, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 51187 / % possible obs: 100 % / Redundancy: 14.2 % / Biso Wilson estimate: 30.74 Å2 / Rmerge(I) obs: 0.096 / Rpim(I) all: 0.027 / Rrim(I) all: 0.1 / Χ2: 0.974 / Net I/σ(I): 6.5
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.0714.40.70227110.9350.190.7270.763100
2.07-2.1513.70.51326910.9540.1430.5330.786100
2.15-2.2514.10.38427340.9730.1050.3990.83100
2.25-2.37150.28227400.9930.0750.2920.861100
2.37-2.5214.80.22427400.9920.060.2310.946100
2.52-2.7114.40.16127390.9950.0440.1671.051100
2.71-2.9913.90.11827860.9970.0320.1221.213100
2.99-3.4214.90.08827940.9980.0230.0911.188100
3.42-4.3113.50.06528430.9980.0180.0681.044100
4.31-5013.40.06130480.9860.0170.0631.03599.8

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→50 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.24
RfactorNum. reflection% reflection
Rfree0.2283 3704 7.24 %
Rwork0.1918 --
obs0.1944 51187 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 90.98 Å2 / Biso mean: 37.2673 Å2 / Biso min: 15.76 Å2
Refinement stepCycle: final / Resolution: 2.001→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3120 0 2 101 3223
Biso mean--34.49 32.17 -
Num. residues----385
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0015-2.02780.30891410.2522178899
2.0278-2.05560.29141470.24681870100
2.0556-2.08490.28631410.24751785100
2.0849-2.11610.21781420.23461806100
2.1161-2.14910.28581460.22841867100
2.1491-2.18440.30231380.2271808100
2.1844-2.2220.24161430.21831811100
2.222-2.26240.25681450.22461823100
2.2624-2.30590.28221430.20941809100
2.3059-2.3530.2641480.21211884100
2.353-2.40410.27091370.21011795100
2.4041-2.460.28091460.21831846100
2.46-2.52160.26571420.2091823100
2.5216-2.58970.23711360.20651826100
2.5897-2.66590.3181460.21481824100
2.6659-2.75190.24781470.21131849100
2.7519-2.85020.27161420.21751816100
2.8502-2.96430.23851430.21211820100
2.9643-3.09920.25851420.2141821100
3.0992-3.26250.24341360.20781832100
3.2625-3.46670.2091440.19271841100
3.4667-3.73420.22321420.17951826100
3.7342-4.10950.16651410.16111840100
4.1095-4.70310.16441390.14591818100
4.7031-5.92160.16221420.1611829100
5.9216-500.2381450.16931826100
Refinement TLS params.Method: refined / Origin x: 6.7499 Å / Origin y: -10.175 Å / Origin z: -9.3593 Å
111213212223313233
T0.127 Å20.0233 Å20.0367 Å2-0.1635 Å20.014 Å2--0.2482 Å2
L0.8376 °20.1527 °20.3687 °2-0.9475 °20.3378 °2--3.3868 °2
S-0.0296 Å °0.0105 Å °-0.0152 Å °0.0035 Å °0.0275 Å °-0.1298 Å °0.083 Å °0.1834 Å °0.0004 Å °
Refinement TLS groupSelection details: all

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