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- PDB-2vju: Crystal structure of the IS608 transposase in complex with the co... -

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Basic information

Entry
Database: PDB / ID: 2vju
TitleCrystal structure of the IS608 transposase in complex with the complete Right end 35-mer DNA and manganese
Components
  • RIGHT END 35-MER
  • TRANSPOSASE ORFA
KeywordsDNA BINDING PROTEIN / PROTEIN-DNA COMPLEX / DNA-BINDING PROTEIN / HUH MOTIF / DNA STEM LOOP / TRANSPOSITION
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA binding / metal ion binding
Similarity search - Function
Transposase IS200 like / Transposase IS200-like / Transposase IS200-like / Transposase IS200-like superfamily / Transposase IS200 like / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Transposase
Similarity search - Component
Biological speciesHELICOBACTER PYLORI (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsBarabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Mechanism of is200/is605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection.
Authors: Barabas, O. / Ronning, D.R. / Guynet, C. / Hickman, A.B. / Ton-Hoang, B. / Chandler, M. / Dyda, F.
History
DepositionDec 13, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSPOSASE ORFA
B: TRANSPOSASE ORFA
C: RIGHT END 35-MER
D: RIGHT END 35-MER
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5567
Polymers58,3914
Non-polymers1653
Water3,279182
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6110 Å2
ΔGint-46 kcal/mol
Surface area22830 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.550, 95.705, 98.561
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.999909, -0.008068, 0.010789), (-0.008856, -0.209802, -0.977704), (0.010152, -0.977711, 0.209711)28.014, 85.002, 68.209
2given(-0.998262, -0.048737, 0.03313), (-0.023089, -0.19378, -0.980773), (0.05422, -0.979834, 0.192318)28.741, 84.579, 68.593

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Components

#1: Protein TRANSPOSASE ORFA / IS608 TRANSPOSASE


Mass: 18392.430 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HELICOBACTER PYLORI (bacteria) / Strain: PECAN2A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q933Z0
#2: DNA chain RIGHT END 35-MER


Mass: 10802.956 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#3: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Compound detailsBASES DC C -3, DG C -35 AND DG C -9 FORM A BASE TRIPLET BASES DT C -4, DA C -34 AND DA C -10 FORM A ...BASES DC C -3, DG C -35 AND DG C -9 FORM A BASE TRIPLET BASES DT C -4, DA C -34 AND DA C -10 FORM A BASE TRIPLET BASES DC D -3, DG D -35 AND DG D -9 FORM A BASE TRIPLET BASES DT D -4, DA D -34 AND DA D -10 FORM A BASE TRIPLET
Sequence detailsTHE ADDITION OF THE FIRST 5 RESIDUES (GSAMA) TO THE DATABASE SEQUENCE ARE THE RESULT OF CLONING ARTIFACT

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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: 2.35 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growpH: 5.5
Details: 20-25% PEG 3350, 0.1 M MES PH 5.5, AND 0.1 M AMMONIUM ACETATE

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Nov 20, 2006 / Details: MULTILAYER FOCUSING MIRROR
RadiationMonochromator: MULTILAYER FOCUSING MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 22916 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 28.1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.7 / % possible all: 94.9

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Processing

Software
NameVersionClassification
CNX2005refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VIH

2vih


Resolution: 2.4→20.04 Å / Rfactor Rfree error: 0.008 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.231 844 3.9 %RANDOM
Rwork0.186 ---
obs-21562 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 22.5054 Å2 / ksol: 0.335087 e/Å3
Displacement parametersBiso mean: 30 Å2
Baniso -1Baniso -2Baniso -3
1-1.84 Å20 Å20 Å2
2---1.2 Å20 Å2
3----0.64 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.4→20.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 1434 3 182 3763
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg2.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.32
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.871.5
X-RAY DIFFRACTIONc_mcangle_it3.112
X-RAY DIFFRACTIONc_scbond_it8.232
X-RAY DIFFRACTIONc_scangle_it8.372.5
LS refinement shellResolution: 2.4→2.51 Å / Rfactor Rfree error: 0.034 / Total num. of bins used: 8
Rfactor% reflection
Rfree0.318 3.5 %
Rwork0.283 -
obs-90.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: ION.TOP

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