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- PDB-5d16: Structure of the C-terminal domain of TnsE double mutant - A453V/D523N -

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Basic information

Entry
Database: PDB / ID: 5d16
TitleStructure of the C-terminal domain of TnsE double mutant - A453V/D523N
ComponentsTransposon Tn7 transposition protein TnsE
KeywordsDNA BINDING PROTEIN / transposition / Tn7 / conformational toggle
Function / homologyTransposition, TnsE / TnsE, C-terminal / TnsE C-terminal domain / transposition / DNA recombination / DNA binding / Transposon Tn7 transposition protein TnsE
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsGuarne, A. / Caron, J.J.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP-67189 Canada
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Conformational toggling controls target site choice for the heteromeric transposase element Tn7.
Authors: Shi, Q. / Straus, M.R. / Caron, J.J. / Wang, H. / Chung, Y.S. / Guarne, A. / Peters, J.E.
History
DepositionAug 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 30, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2015Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 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
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: Transposon Tn7 transposition protein TnsE
B: Transposon Tn7 transposition protein TnsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3303
Polymers46,2382
Non-polymers921
Water3,639202
1
A: Transposon Tn7 transposition protein TnsE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,2112
Polymers23,1191
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transposon Tn7 transposition protein TnsE


Theoretical massNumber of molelcules
Total (without water)23,1191
Polymers23,1191
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 71.250, 50.430
Angle α, β, γ (deg.)90.00, 97.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Transposon Tn7 transposition protein TnsE / Protein D


Mass: 23118.994 Da / Num. of mol.: 2 / Fragment: C-terminal domain (UNP residues 342-538) / Mutation: A453V, D523N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnsE / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P05845
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 202 / 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: 1.81 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: PEG 3350, Bis-Tris / PH range: 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Jun 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.76→32.49 Å / Num. all: 32735 / Num. obs: 32735 / % possible obs: 99.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 21
Reflection shellResolution: 1.76→1.82 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.973 / Mean I/σ(I) obs: 1.4 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5D17

5d17


Resolution: 1.76→29.301 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 27.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 1637 5.01 %Random selection
Rwork0.1977 ---
obs0.1988 32706 99.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.76→29.301 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2426 0 6 202 2634
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0042495
X-RAY DIFFRACTIONf_angle_d0.7573381
X-RAY DIFFRACTIONf_dihedral_angle_d13.023893
X-RAY DIFFRACTIONf_chiral_restr0.029384
X-RAY DIFFRACTIONf_plane_restr0.003438
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.81180.34691370.36952593X-RAY DIFFRACTION100
1.8118-1.87030.35811350.33542577X-RAY DIFFRACTION100
1.8703-1.93710.29131370.28262579X-RAY DIFFRACTION100
1.9371-2.01460.29291350.24872558X-RAY DIFFRACTION100
2.0146-2.10630.26971350.23422566X-RAY DIFFRACTION100
2.1063-2.21730.23161360.22542585X-RAY DIFFRACTION100
2.2173-2.35620.27031370.22182597X-RAY DIFFRACTION100
2.3562-2.5380.24891350.21322578X-RAY DIFFRACTION100
2.538-2.79320.2671360.21812586X-RAY DIFFRACTION100
2.7932-3.1970.21061380.20232608X-RAY DIFFRACTION100
3.197-4.02620.19951370.17582603X-RAY DIFFRACTION100
4.0262-29.30550.17081390.15422639X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.76-0.74690.60891.4960.4351.4699-0.01140.48820.0277-0.2062-0.0588-0.0058-0.1135-0.0973-0.00290.3921-0.0492-0.04990.33440.10370.3838-15.6186-6.1028-12.7682
21.60560.9390.13741.33330.62662.1991-0.0772-0.06680.06680.1670.0568-0.0089-0.1952-0.09720.00020.3296-0.03160.01480.27150.09220.2725-17.5793-6.8518-5.7349
30.532-0.0692-0.12550.09640.2140.6284-0.1559-0.4744-0.65180.66370.60671.06640.0387-0.44470.17850.43410.0520.13810.39930.22820.5426-23.8042-9.63420.6612
41.87470.7251-1.58733.5153.3257.3633-0.0291-0.6113-0.2210.7520.3194-0.18430.00230.40210.90150.79020.07620.10520.41410.30660.3676-15.1755-16.08626.8565
50.41710.0049-0.50511.07850.39511.3378-0.0912-0.0710.93290.13560.0181-0.4091-0.4163-0.0859-0.01910.535-0.0195-0.09370.37650.16450.7898-7.44413.1768-3.2737
60.6007-0.1992-0.10510.79290.63650.4843-0.0616-0.42040.43630.4866-0.1684-0.3675-0.20010.2221-0.01180.4361-0.0607-0.10670.39740.00780.6828-1.5803-3.8692-0.7424
70.50750.03140.57981.9064-0.69520.9544-0.10390.1716-0.4606-0.4732-0.04960.09740.09380.76530.00580.3882-0.03980.04260.7934-0.1130.4599-4.1939-36.2597-23.4892
81.67610.4124-1.15392.31291.61072.7601-0.08330.4057-0.4142-0.1933-0.17080.0918-0.18230.4479-0.00020.3285-0.086-0.02710.4321-0.00080.3645-7.4148-33.2274-16.3454
90.5216-0.483-0.82721.09260.6671.2116-0.28280.0362-0.1080.08990.03910.2116-0.55490.53330.00040.3994-0.0892-0.02850.33360.08650.3423-9.1483-27.8883-7.6906
100.0218-0.1096-0.03791.7699-0.33280.60840.49860.94990.7097-0.9591-0.0528-0.4227-0.39850.19760.11490.7706-0.26710.1221.3820.34860.25551.7432-21.3039-23.7002
110.406-0.2882-0.27470.67990.5130.3960.00490.08170.5404-0.33510.3128-0.2976-0.2096-0.01580.16950.4526-0.56840.15591.6637-0.01190.50478.6227-25.5416-20.6369
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 377:420
2X-RAY DIFFRACTION2chain A and resid 421:474
3X-RAY DIFFRACTION3chain A and resid 475:496
4X-RAY DIFFRACTION4chain A and resid 497:503
5X-RAY DIFFRACTION5chain A and resid 504:522
6X-RAY DIFFRACTION6chain A and resid 523:537
7X-RAY DIFFRACTION7chain B and resid 377:420
8X-RAY DIFFRACTION8chain B and resid 421:481
9X-RAY DIFFRACTION9chain B and resid 482:505
10X-RAY DIFFRACTION10chain B and resid 506:520
11X-RAY DIFFRACTION11chain B and resid 521:533

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