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- PDB-1f1z: TNSA, a catalytic component of the TN7 transposition system -

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Basic information

Entry
Database: PDB / ID: 1f1z
TitleTNSA, a catalytic component of the TN7 transposition system
ComponentsTNSA ENDONUCLEASE
KeywordsDNA BINDING PROTEIN / restriction endonuclease fold
Function / homology
Function and homology information


transposase activity / DNA transposition / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / chromosome / endonuclease activity / DNA binding / metal ion binding
Similarity search - Function
TnsA endonuclease C-terminal / TnsA endonuclease, N-terminal / TnsA endonuclease C terminal / TnsA-like endonuclease N terminal / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A ...TnsA endonuclease C-terminal / TnsA endonuclease, N-terminal / TnsA endonuclease C terminal / TnsA-like endonuclease N terminal / Trna Endonuclease; Chain: A, domain 1 - #10 / Trna Endonuclease; Chain: A, domain 1 / tRNA endonuclease-like domain superfamily / Restriction endonuclease type II-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Transposon Tn7 transposition protein TnsA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsHickman, A.B. / Li, Y. / Mathew, S.V. / May, E.W. / Craig, N.L. / Dyda, F.
CitationJournal: Mol.Cell / Year: 2000
Title: Unexpected structural diversity in DNA recombination: the restriction endonuclease connection.
Authors: Hickman, A.B. / Li, Y. / Mathew, S.V. / May, E.W. / Craig, N.L. / Dyda, F.
History
DepositionMay 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 28, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TNSA ENDONUCLEASE
B: TNSA ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7628
Polymers62,5932
Non-polymers1686
Water5,260292
1
A: TNSA ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3814
Polymers31,2971
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TNSA ENDONUCLEASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3814
Polymers31,2971
Non-polymers843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.35, 83.68, 97.94
Angle α, β, γ (deg.)90.0, 94.07, 90.0
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TNSA ENDONUCLEASE / TRANSPOSASE


Mass: 31296.697 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / Cell line: XA90 / References: UniProt: P13988
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 50.88 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG 8000, Isopropanol, MgCl2, NaCl, Tris-HCl HEPES, Triton X100, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
17-8 mg/mlprotein1drop
225 mMHEPES1drop
30.5 M1dropNaCl
41 mMEDTA1drop
52 mMdithiothreitol1drop
60.01 %(v/v)Tritron X-1001drop
710 %(w/v)glycerol1drop
810 %(v/v)isopropanol1drop
9buffer 11drop
1010 %PEG80001buffer 1
110.1 MTris-HCl1buffer 1
1250 mM1buffer 1MgCl2
130.1 M1reservoirNaCl
1410 %isopropanol1reservoir
15buffer 11reservoir90 %

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Oct 2, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 131670 / Num. obs: 131670 / % possible obs: 97 % / Observed criterion σ(F): -6 / Observed criterion σ(I): -3 / Redundancy: 5.58 % / Biso Wilson estimate: 28.45 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 13.2
Reflection shellResolution: 2.4→2.47 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.197 / Num. unique all: 23511 / % possible all: 80.7
Reflection
*PLUS
Num. obs: 23596 / Num. measured all: 131670
Reflection shell
*PLUS
% possible obs: 80.7 %

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASESphasing
X-PLOR3.1refinement
RefinementResolution: 2.4→30 Å / σ(F): 2 / σ(I): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1114 -random
Rwork0.202 ---
all0.205 23511 --
obs0.202 22878 97 %-
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4190 0 6 291 4487
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.676

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