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- PDB-2xm3: Deinococcus radiodurans ISDra2 Transposase Left end DNA complex -

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Basic information

Entry
Database: PDB / ID: 2xm3
TitleDeinococcus radiodurans ISDra2 Transposase Left end DNA complex
Components
  • 5'-D(*TP*TP*AP*GP*T)-3'
  • DRA2 TRANSPOSASE BINDING ELEMENT
  • 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
ACETATE ION / DNA / DNA (> 10) / ISDra2 transposase TnpA
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SIRAS / 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 22, 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 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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.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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TRANSPOSASE
B: TRANSPOSASE
C: TRANSPOSASE
D: TRANSPOSASE
E: TRANSPOSASE
F: TRANSPOSASE
G: DRA2 TRANSPOSASE BINDING ELEMENT
H: 5'-D(*TP*TP*AP*GP*T)-3'
I: DRA2 TRANSPOSASE BINDING ELEMENT
J: 5'-D(*TP*TP*AP*GP*T)-3'
K: DRA2 TRANSPOSASE BINDING ELEMENT
L: 5'-D(*TP*TP*AP*GP*T)-3'
M: DRA2 TRANSPOSASE BINDING ELEMENT
N: 5'-D(*TP*TP*AP*GP*T)-3'
O: DRA2 TRANSPOSASE BINDING ELEMENT
P: 5'-D(*TP*TP*AP*GP*T)-3'
Q: DRA2 TRANSPOSASE BINDING ELEMENT
R: 5'-D(*TP*TP*AP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,10835
Polymers155,38918
Non-polymers71917
Water9,170509
1
C: TRANSPOSASE
D: TRANSPOSASE
K: DRA2 TRANSPOSASE BINDING ELEMENT
L: 5'-D(*TP*TP*AP*GP*T)-3'
M: DRA2 TRANSPOSASE BINDING ELEMENT
N: 5'-D(*TP*TP*AP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98611
Polymers51,7966
Non-polymers1895
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8690 Å2
ΔGint-91.1 kcal/mol
Surface area17920 Å2
MethodPISA
2
A: TRANSPOSASE
B: TRANSPOSASE
G: DRA2 TRANSPOSASE BINDING ELEMENT
H: 5'-D(*TP*TP*AP*GP*T)-3'
I: DRA2 TRANSPOSASE BINDING ELEMENT
J: 5'-D(*TP*TP*AP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,13713
Polymers51,7966
Non-polymers3407
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8890 Å2
ΔGint-92.9 kcal/mol
Surface area17920 Å2
MethodPISA
3
E: TRANSPOSASE
F: TRANSPOSASE
O: DRA2 TRANSPOSASE BINDING ELEMENT
P: 5'-D(*TP*TP*AP*GP*T)-3'
Q: DRA2 TRANSPOSASE BINDING ELEMENT
R: 5'-D(*TP*TP*AP*GP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,98611
Polymers51,7966
Non-polymers1895
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-87.4 kcal/mol
Surface area17720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.583, 128.384, 140.222
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
TRANSPOSASE / / DRA2 TRANSPOSASE


Mass: 16135.772 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: ISDRA2 INSERTION SEQUENCE
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O83028

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DNA chain , 2 types, 12 molecules GIKMOQHJLNPR

#2: DNA chain
DRA2 TRANSPOSASE BINDING ELEMENT


Mass: 8252.322 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain
5'-D(*TP*TP*AP*GP*T)-3' / DRA2 TRANSPOSASE LEFT END CLEAVAGE SITE


Mass: 1510.034 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: ISDRA2 INSERTION SEQUENCE LEFT END FLANK / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 4 types, 526 molecules

#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 509 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsTRANSPOSON SEQUENCE DEINOCOCCUS RADIODURANS SEQUNCE USED AS TARGET SITE BY DRA2 TRANSPOSON

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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: 2.99 Å3/Da / Density % sol: 58.96 % / Description: NONE
Crystal growTemperature: 292 K / pH: 4.6
Details: COMPLEX BUFFER: 25 MM TRIS/HCL PH 8.0, 0.15M NACL PRECIPITATING AGENT: 17% PEG 6000, 50 MM NAACETATE PH 4.6 10MG/ML COMPLEX MIXED WITH EQUAL AMOUNT OF PRECIPITATING AGENT AT 19 C, ...Details: COMPLEX BUFFER: 25 MM TRIS/HCL PH 8.0, 0.15M NACL PRECIPITATING AGENT: 17% PEG 6000, 50 MM NAACETATE PH 4.6 10MG/ML COMPLEX MIXED WITH EQUAL AMOUNT OF PRECIPITATING AGENT AT 19 C, CRYOPROTECTED WITH 15-20% 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: Sep 14, 2007 / Details: MULTILAYER 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: 84171 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 6.84 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.9
Reflection shellResolution: 2.3→2.37 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.83 / Mean I/σ(I) obs: 2.41 / % possible all: 97.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASESphasing
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 2.3→30 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2489 1575 1.9 %RANDOM
Rwork0.2179 ---
obs0.2179 78520 93.1 %-
Solvent computationSolvent model: FLAT MODE / Bsol: 29.1693 Å2 / ksol: 0.324567 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.813 Å20 Å20 Å2
2--6.292 Å20 Å2
3----7.105 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6165 3882 40 509 10596
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009419
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_deg4.09917
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 file
X-RAY DIFFRACTION1PARHCSDX.PRO
X-RAY DIFFRACTION2PARAM19.SOL
X-RAY DIFFRACTION3DNA-RNA_REP.PARAM
X-RAY DIFFRACTION4MO4_XPLOR_H.PAR
X-RAY DIFFRACTION5ACY_XPLOR.PAR

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