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- PDB-2vjv: Crystal structure of the IS608 transposase in complex with left e... -

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Basic information

Entry
Database: PDB / ID: 2vjv
TitleCrystal structure of the IS608 transposase in complex with left end 26-mer DNA hairpin and a 6-mer DNA representing the left end cleavage site
Components
  • 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3'
  • 5'-D(*DT*DA*DT*DT*DA*DCP)-3'
  • TRANSPOSASE ORFA
KeywordsDNA BINDING PROTEIN / DNA-BINDING PROTEIN / PROTEIN-DNA COMPLEX / 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: 1.9 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.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.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

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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: 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3'
D: 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3'
E: 5'-D(*DT*DA*DT*DT*DA*DCP)-3'
F: 5'-D(*DT*DA*DT*DT*DA*DCP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,4319
Polymers56,3586
Non-polymers733
Water4,954275
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9430 Å2
ΔGint-30.2 kcal/mol
Surface area20950 Å2
MethodPQS
Unit cell
Length a, b, c (Å)66.292, 72.407, 110.174
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.985391, 0.170267, -0.003787), (0.170025, 0.984788, 0.035829), (0.00983, 0.034662, -0.999351)
Vector: 33.591, -3.887, 57.719)

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Components

#1: Protein TRANSPOSASE ORFA / IS608 TRANSPOSASE


Mass: 18392.430 Da / Num. of mol.: 2 / Fragment: RESIDUES 2-155
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 5'-D(*DA*DA*DA*DG*DC*DC*DC*DC*DT*DA*DG*DC*DTP*DT *DT*DT*DA*DG*DC*DT*DA*DT*DG*DG*DG*DGP)-3' / LEFT END 26-MER HAIRPIN


Mass: 8003.165 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#3: DNA chain 5'-D(*DT*DA*DT*DT*DA*DCP)-3' / 6-MER LEFT END CLEAVAGE SITE


Mass: 1783.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HELICOBACTER PYLORI (bacteria)
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / Source method: isolated from a natural source / Formula: H2O
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: 2.29 Å3/Da / Density % sol: 50.75 % / Description: NONE
Crystal growpH: 5 / Details: 6-10% PEG 600 AND 50 MM SODIUM CITRATE PH 5.0

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Jun 12, 2007 / Details: MULTILAYER FOCUSING OPTICS
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: 1.9→40 Å / Num. obs: 38044 / % possible obs: 89.8 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Biso Wilson estimate: 17.3 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 11.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 4.6 / % possible all: 64.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VIH

2vih


Resolution: 1.9→24.61 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1368904.85 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.227 1131 3 %RANDOM
Rwork0.194 ---
obs0.194 37220 87.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.2464 Å2 / ksol: 0.353019 e/Å3
Displacement parametersBiso mean: 29.6 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--1.98 Å20 Å2
3----0.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 1.9→24.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 1298 3 275 3622
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_deg3.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.39
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.761.5
X-RAY DIFFRACTIONc_mcangle_it3.012
X-RAY DIFFRACTIONc_scbond_it9.782
X-RAY DIFFRACTIONc_scangle_it8.982.5
LS refinement shellResolution: 1.9→1.97 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.322 78 3 %
Rwork0.325 2497 -
obs--61.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLWATER.TOP
X-RAY DIFFRACTION4MO4_XPLOR_PAR.TXTMO4_XPLOR_TOP.TXT

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