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- PDB-2xqc: DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT EN... -

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Basic information

Entry
Database: PDB / ID: 2xqc
TitleDEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE COMPLEXED WITH LEFT END RECOGNITION AND CLEAVAGE SITE AND ZN
Components
  • 5'-D(TP*TP*GP*AP*TP*GP)-3'
  • DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
  • TRANSPOSASE
KeywordsDNA BINDING PROTEIN/DNA / DNA BINDING PROTEIN-DNA COMPLEX / TRANSPOSITION / MOBILE ELEMENT
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / 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) / ISDra2 transposase TnpA
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F.
CitationJournal: Embo J. / Year: 2010
Title: DNA Recognition and the Precleavage State During Single-Stranded DNA Transposition in D. Radiodurans.
Authors: Hickman, A.B. / James, J.A. / Barabas, O. / Pasternak, C. / Ton-Hoang, B. / Chandler, M. / Sommer, S. / Dyda, F.
History
DepositionSep 1, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 13, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation
Category: exptl_crystal_grow / pdbx_seq_map_depositor_info / struct_biol
Item: _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details ..._exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details / _exptl_crystal_grow.temp / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.5Dec 20, 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 / struct_site
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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSPOSASE
B: DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
C: 5'-D(TP*TP*GP*AP*TP*GP)-3'
D: TRANSPOSASE
E: DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE
F: 5'-D(TP*TP*GP*AP*TP*GP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,04315
Polymers52,4556
Non-polymers5899
Water8,539474
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13020 Å2
ΔGint-337.1 kcal/mol
Surface area17630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.762, 92.716, 126.070
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TRANSPOSASE / / DRA2 TRANSPOSASE


Mass: 16135.772 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83028
#2: DNA chain DRA2 TRANSPOSASE LEFT END RECOGNITION SEQUENCE


Mass: 8252.322 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: ISDRA2 TRANSPOSON INTERNAL SEQUENCE / Source: (synth.) DEINOCOCCUS RADIODURANS (radioresistant)
#3: DNA chain 5'-D(TP*TP*GP*AP*TP*GP)-3' / DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE / F


Mass: 1839.239 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) DEINOCOCCUS RADIODURANS (radioresistant)
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 474 / 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: 2.77 Å3/Da / Density % sol: 55.63 % / Description: NONE
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: COMPLEX BUFFER: 35MM TRIS-HCL PH8.0, 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. THE TERNARY COMPLEX WAS FORMED BY MIXING PROTEIN AT 9MG/ML WITH THE LE BINDING SITE DNA AND CLEAVAGE SITE DNA AT A ...Details: COMPLEX BUFFER: 35MM TRIS-HCL PH8.0, 0.15M NACL, 10MM MGCL2, 0.5 MM TCEP. THE TERNARY COMPLEX WAS FORMED BY MIXING PROTEIN AT 9MG/ML WITH THE LE BINDING SITE DNA AND CLEAVAGE SITE DNA AT A RATIO OF 1:1.1:1.3 CRYSTALS WERE OBTAINED AT 19C BY MIXING THE COMPLEX AT 1:1 WITH WELL SOLUTION OF 10MM ZNCL2, 0.1M NA-ACETATE PH 4.2, 17& PEG 4000. CRYSTALS WERE CRYOPROTECTED IN 20% GLYCEROL.

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 17, 1998 / Details: MULTILAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 45279 / % possible obs: 96.7 % / Observed criterion σ(I): -3 / Redundancy: 7.24 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.49 / % possible all: 75.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XO6

2xo6


Resolution: 1.9→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2089 900 1.9 %RANDOM
Rwork0.1758 ---
obs0.1758 44429 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.6875 Å2 / ksol: 0.33546 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.189 Å20 Å20 Å2
2--4.103 Å20 Å2
3---0.086 Å2
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2106 1338 9 474 3927
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012338
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_deg4.8032
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3METALS_XPLOR_H.PARMETALS_XPLOR_H.TOP
X-RAY DIFFRACTION4PARAM19.SOLTOPH19_MOD.SOL

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