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- PDB-3ecp: Crystal Structure Of Tn5 Transposase Complexed With 5' Phosphoryl... -

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Basic information

Entry
Database: PDB / ID: 3ecp
TitleCrystal Structure Of Tn5 Transposase Complexed With 5' Phosphorylated Transposon End DNA
Components
  • DNA non-transferred strand
  • DNA transferred strand
  • Tn5 transposase
KeywordsDNA RECOMBINATION/DNA / TRANSPOSASE / RIBONUCLEASE H-LIKE MOTIF / PROTEIN-DNA COMPLEX / SYNAPTIC COMPLEX / DNA RECOMBINATION-DNA COMPLEX
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
Transposase Tn5, dimerisation / : / Transposase Tn5 dimerisation domain / Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal ...Transposase Tn5, dimerisation / : / Transposase Tn5 dimerisation domain / Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : / Transposase DDE domain / Transposase DNA-binding / Serum Albumin; Chain A, Domain 1 / Ribonuclease H-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposase for transposon Tn5 / Transposase for transposon Tn5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsKlenchin, V.A.
CitationJournal: Nucleic Acids Res. / Year: 2008
Title: Phosphate coordination and movement of DNA in the Tn5 synaptic complex: role of the (R)YREK motif
Authors: Klenchin, V.A. / Czyz, A. / Goryshin, I.Y. / Gradman, R. / Lovell, S. / Rayment, I. / Reznikoff, W.S.
History
DepositionSep 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 29, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tn5 transposase
B: DNA transferred strand
C: DNA non-transferred strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9096
Polymers65,6333
Non-polymers2763
Water2,162120
1
A: Tn5 transposase
B: DNA transferred strand
C: DNA non-transferred strand
hetero molecules

A: Tn5 transposase
B: DNA transferred strand
C: DNA non-transferred strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,81912
Polymers131,2666
Non-polymers5536
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_665-y+1,-x+1,-z+1/61
Buried area19660 Å2
ΔGint-96 kcal/mol
Surface area46960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.508, 113.508, 228.775
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-623-

HOH

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Components

#1: Protein Tn5 transposase


Mass: 53367.047 Da / Num. of mol.: 1 / Fragment: Tn5 transposase / Mutation: E54K, M56A, L372P, G477
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: orf163 / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q08JA5, UniProt: Q46731*PLUS
#2: DNA chain DNA transferred strand


Mass: 6213.039 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRANSPOSASE RECOGNITION SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
#3: DNA chain DNA non-transferred strand


Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: TRANSPOSASE RECOGNITION SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 120 / 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: 3.24 Å3/Da / Density % sol: 62.05 %
Crystal growTemperature: 293 K / pH: 6.5
Details: 13% (w/v) oMe-PEG 5000, 0.1M bis-tris, 0.1M ammonium sulfate, pH 6.5, microbatch, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1oMe-PEG 500011
2bis-tris11
3(NH4)2SO411
4oMe-PEG 500012
5bis-tris12
6(NH4)2SO412

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.00964 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 7, 2006
RadiationMonochromator: Si-111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00964 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 31006 / Num. obs: 30992 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 20.4 % / Biso Wilson estimate: 66.4 Å2 / Rmerge(I) obs: 0.044 / Net I/σ(I): 69.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 18 % / Rmerge(I) obs: 0.379 / Mean I/σ(I) obs: 9 / Num. unique all: 3032 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.2refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MUH

1muh


Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.922 / SU B: 24.704 / SU ML: 0.261 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.359 / ESU R Free: 0.275 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27386 1556 5 %RANDOM
Rwork0.21878 ---
all0.22153 29364 --
obs0.22153 29291 99.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 61.752 Å2
Baniso -1Baniso -2Baniso -3
1--1.87 Å2-0.94 Å20 Å2
2---1.87 Å20 Å2
3---2.81 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3605 818 18 120 4561
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0214619
X-RAY DIFFRACTIONr_angle_refined_deg1.5292.1896404
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9785460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.27523.11164
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.21615675
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3041535
X-RAY DIFFRACTIONr_chiral_restr0.0860.2702
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023167
X-RAY DIFFRACTIONr_nbd_refined0.2130.22051
X-RAY DIFFRACTIONr_nbtor_refined0.3080.23029
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2231
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1170.215
X-RAY DIFFRACTIONr_mcbond_it2.49852346
X-RAY DIFFRACTIONr_mcangle_it3.64963639
X-RAY DIFFRACTIONr_scbond_it3.50472844
X-RAY DIFFRACTIONr_scangle_it4.2567.52763
LS refinement shellResolution: 2.5→2.564 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.385 112 -
Rwork0.342 2105 -
obs--99.91 %
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)
12.0271.03970.25862.24631.12931.77630.06090.468-0.2545-0.19380.3168-0.23590.10.3572-0.3777-0.25320.1315-0.07280.1321-0.3738-0.138936.75138.591-2.716
21.39290.34490.96451.70671.49955.07330.00620.1716-0.38130.1019-0.21570.25430.588-0.67570.2096-0.02340.0223-0.17580.0046-0.25170.123213.9519.9771.459
36.06880.9847-0.43012.3718-0.24021.4717-0.06320.0127-0.8373-0.11470.3936-0.80720.70280.633-0.33040.05780.3733-0.2980.1695-0.49310.356453.49621.48915.892
42.3128-0.49820.51190.8102-0.02654.69990.23330.102-0.39610.06490.31320.03730.38230.26-0.5465-0.05320.153-0.2722-0.1804-0.1778-0.069928.52327.5420.977
51.410.39840.35643.5914-2.28877.01770.0726-0.526-0.53851.39950.5951-0.07730.53350.1341-0.66770.86050.3749-0.53850.1316-0.03060.244237.57615.86548.468
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 214
2X-RAY DIFFRACTION1A321 - 370
3X-RAY DIFFRACTION2A215 - 320
4X-RAY DIFFRACTION3A372 - 477
5X-RAY DIFFRACTION4C1 - 10
6X-RAY DIFFRACTION4B11 - 20
7X-RAY DIFFRACTION5B1 - 10
8X-RAY DIFFRACTION5C11 - 20

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