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- PDB-1mus: crystal structure of Tn5 transposase complexed with resolved outs... -

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Basic information

Entry
Database: PDB / ID: 1mus
Titlecrystal structure of Tn5 transposase complexed with resolved outside end DNA
Components
  • DNA non-transferred strand
  • DNA transferred strand
  • Tn5 transposase
KeywordsTRANSCRIPTION/DNA / transposase / hairpin / dna binding / TRANSCRIPTION-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
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 / : ...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
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHolden, H.M. / Thoden, J.B. / Steiniger-White, M. / Reznikoff, W.S. / Lovell, S. / Rayment, I.
CitationJournal: Curr.Opin.Struct.Biol. / Year: 2004
Title: Structure/function insights into Tn5 transposition.
Authors: Steiniger-White, M. / Rayment, I. / Reznikoff, W.S.
History
DepositionSep 24, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 27, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: 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
B: DNA transferred strand
C: DNA non-transferred strand
A: Tn5 transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,93410
Polymers65,5893
Non-polymers3457
Water11,079615
1
B: DNA transferred strand
C: DNA non-transferred strand
A: Tn5 transposase
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)131,86820
Polymers131,1786
Non-polymers68914
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+5/61
Unit cell
Length a, b, c (Å)112.700, 112.700, 235.900
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-480-

MG

Detailshomodimer, the other half of the dimer may be generated by use of the following rotation matrix and translation vector ROTATION MATRIX: 0.50000 0.86603 0.00000 0.86603 -0.50000 0.00000 0.00000 0.00000 -1.00000 TRANSLATION VECTOR IN AS -0.00045 -0.00055 196.58308

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Components

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DNA chain , 2 types, 2 molecules BC

#1: DNA chain DNA transferred strand


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


Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON

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Protein , 1 types, 1 molecules A

#3: Protein Tn5 transposase


Mass: 53323.102 Da / Num. of mol.: 1 / Mutation: E54K, M56A, D119K, K120A, E345K, L372P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(de3)pLysS / References: UniProt: Q46731

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Non-polymers , 4 types, 622 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 615 / 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: 3.27 Å3/Da / Density % sol: 62.43 %
Crystal growTemperature: 290 K / Method: batch / pH: 7.5
Details: PEG-1500, Hepes, manganese chloride, magnesium chloride, pH 7.5, batch, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG-150011
2Hepes11
3MnCl211
4MgCl211
5MnCl212
6MgCl212
Crystal grow
*PLUS
pH: 7.7 / Method: batch method / Details: Davies, D.R., (2000) Science, 289, 77.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
10.3 M1dropKCl
220 mMHEPES1droppH7.7
32 mMEDTA1drop
410 mg/mlprotein1drop
530 %(w/v)PEG4001reservoir
6100 mMMES1reservoirpH6.0
760 mMammonium sulfate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.95 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 12, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 61106 / Num. obs: 61106 / % possible obs: 86.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rsym value: 0.063 / Net I/σ(I): 34.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 4.9 / Num. unique all: 4221 / Rsym value: 0.224 / % possible all: 61.2
Reflection
*PLUS

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Processing

Software
NameClassification
DENZOdata reduction
HKL-2000data reduction
EPMRphasing
TNTrefinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1F3I

1f3i
PDB Unreleased entry


Resolution: 1.9→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.249 5942 10 %random
Rwork0.191 ---
all0.193 60265 --
obs0.193 60265 85.5 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3611 818 16 615 5060
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.38
Refinement
*PLUS
% reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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