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- PDB-2xma: DEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE RIGHT END DNA COMPLEX -

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Basic information

Entry
Database: PDB / ID: 2xma
TitleDEINOCOCCUS RADIODURANS ISDRA2 TRANSPOSASE RIGHT END DNA COMPLEX
Components
  • DRA2 TRANSPOSASE RIGHT END RECOGNITION SITE
  • 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: 2.3 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
DepositionJul 26, 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 1.4Dec 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_sheet / 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.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_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_sheet.number_strands / _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: TRANSPOSASE
C: DRA2 TRANSPOSASE RIGHT END RECOGNITION SITE
D: DRA2 TRANSPOSASE RIGHT END RECOGNITION SITE
E: TRANSPOSASE
F: TRANSPOSASE
G: DRA2 TRANSPOSASE RIGHT END RECOGNITION SITE
H: DRA2 TRANSPOSASE RIGHT END RECOGNITION SITE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,92512
Polymers107,8278
Non-polymers974
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25300 Å2
ΔGint-191.6 kcal/mol
Surface area36670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.827, 89.288, 90.104
Angle α, β, γ (deg.)90.00, 111.23, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.580052, -0.376478, -0.722361), (-0.399438, -0.641396, 0.655027), (-0.709922, 0.668488, 0.221663)26.5424, 2.6303, 14.2016
2given(-0.996574, 0.039401, 0.072719), (-0.022909, 0.713337, -0.700447), (-0.079471, -0.699713, -0.70999)4.6756, 20.3683, 49.8023
3given(0.643202, 0.224422, 0.732069), (0.36283, -0.93126, -0.033301), (0.674273, 0.287036, -0.680416)-19.8202, 19.8929, 35.7988
4given(-0.567727, -0.373218, -0.733754), (-0.4131, -0.641815, 0.646082), (-0.712063, 0.669912, 0.210199)26.6269, 2.6508, 14.2999
5given(-0.713754, -0.247609, -0.655168), (-0.151779, -0.858515, 0.489812), (-0.683754, 0.449046, 0.575186)24.9716, 7.6297, 7.8199

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Components

#1: Protein
TRANSPOSASE / / DRA2 TRANSPOSASE


Mass: 16418.049 Da / Num. of mol.: 4
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 RIGHT END RECOGNITION SITE


Mass: 10538.786 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: ISDRA2 TRANSPOSON SEQUENCE / Source: (synth.) DEINOCOCCUS RADIODURANS (radioresistant)
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsIN CHAINS A,E,F THE RENMANTS OF THE NTERM HIS TAG CLEAVAGE BY THROMBIN ARE VISIBLE IN THE ELECTRON ...IN CHAINS A,E,F THE RENMANTS OF THE NTERM HIS TAG CLEAVAGE BY THROMBIN ARE VISIBLE IN THE ELECTRON DENSITY. THESE RESIDUES ARE -2 GLY -1 SER 0 HIS IN CHAINS A,E,F DEINOCOCCUS RADIODURANS ISDRA2 TRANPOSON INTERNAL SEQUENCE

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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: 2.67 Å3/Da / Density % sol: 53.96 % / Description: NONE
Crystal growpH: 8
Details: COMLEX BUFFER: 35MM TRIS-HCL PH 8.O, 0.1 M NA-MALONATE 10MM MGCL2M 0.5 MM TCEP PRECIPITATING AGENT: 0.16 MM MGCL2, 0.1 M TRIS-HCL PH 7.9, 3.4M 1,6-HEXANEDIOL FROZEN IN LIQUID PROPANE W/O ...Details: COMLEX BUFFER: 35MM TRIS-HCL PH 8.O, 0.1 M NA-MALONATE 10MM MGCL2M 0.5 MM TCEP PRECIPITATING AGENT: 0.16 MM MGCL2, 0.1 M TRIS-HCL PH 7.9, 3.4M 1,6-HEXANEDIOL FROZEN IN LIQUID PROPANE W/O ADDITIONAL CRYOPROTECTION

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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: Mar 17, 2008 / Details: MULTI-LAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 50130 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 3.62 % / Rsym value: 0.05 / Net I/σ(I): 16.4
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 3.09 / Rsym value: 0.39 / % possible all: 99

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XM3

2xm3


Resolution: 2.3→30 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 953 1.9 %RANDOM
Rwork0.2152 ---
obs0.2152 47910 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 39.9151 Å2 / ksol: 0.312105 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.051 Å20 Å24.602 Å2
2---1.034 Å20 Å2
3---4.085 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4458 2778 4 229 7469
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005776
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_deg2.77184
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
Refine LS restraints NCSNCS model details: RESTRAINTS
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2DNA-RNA_REP_NOPUCKERS.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3PARAM19.SOLTOPH19_MOD.SOL
X-RAY DIFFRACTION4MO4_XPLOR_H.PARMO4_XPLOR_H.TOP

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