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- PDB-2ec2: Crystal structure of transposase from Sulfolobus tokodaii -

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Basic information

Entry
Database: PDB / ID: 2ec2
TitleCrystal structure of transposase from Sulfolobus tokodaii
Components136aa long hypothetical transposase
KeywordsGENE REGULATION / Transposase / Sulfolobus tokodaii
Function / homology
Function and homology information


transposase activity / DNA transposition / DNA 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
Transposase for insertion sequence element
Similarity search - Component
Biological speciesSulfolobus tokodaii (archaea)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKawai, K. / Suzuki, A. / Kuramitsu, S. / Masui, R. / Yamane, T.
CitationJournal: To be Published
Title: Crystal structure of transposase from Sulfolobus tokodaii
Authors: Kawai, K. / Suzuki, A. / Kuramitsu, S. / Masui, R. / Yamane, T.
History
DepositionFeb 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 136aa long hypothetical transposase
B: 136aa long hypothetical transposase
C: 136aa long hypothetical transposase
D: 136aa long hypothetical transposase
E: 136aa long hypothetical transposase
F: 136aa long hypothetical transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,22114
Polymers96,4536
Non-polymers7698
Water00
1
A: 136aa long hypothetical transposase
C: 136aa long hypothetical transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4395
Polymers32,1512
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-60 kcal/mol
Surface area13480 Å2
MethodPISA
2
B: 136aa long hypothetical transposase
D: 136aa long hypothetical transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4395
Polymers32,1512
Non-polymers2883
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4020 Å2
ΔGint-61 kcal/mol
Surface area13550 Å2
MethodPISA
3
E: 136aa long hypothetical transposase
F: 136aa long hypothetical transposase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3434
Polymers32,1512
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3860 Å2
ΔGint-41 kcal/mol
Surface area13200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.118, 66.566, 69.472
Angle α, β, γ (deg.)107.96, 104.39, 110.72
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
136aa long hypothetical transposase


Mass: 16075.478 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus tokodaii (archaea) / Plasmid: plasmid / Production host: Escherichia coli (E. coli) / References: UniProt: Q974H8
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% PEG 4000, 0.2M Lithium Sulfate, 0.1M Sodium Acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Mar 10, 2006
RadiationMonochromator: CONFOCAL MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→80 Å / Num. all: 19864 / Num. obs: 18474 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.057 / Net I/σ(I): 28.1
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.23 / % possible all: 82

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
CrystalClear(MSC/RIGAKU)data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F5G

2f5g


Resolution: 2.8→25.78 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.812 / SU B: 18.591 / SU ML: 0.383 / Cross valid method: THROUGHOUT / ESU R Free: 0.531 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29861 945 5.1 %RANDOM
Rwork0.20136 ---
obs0.20629 17502 93.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 44.571 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-1.46 Å2-0.56 Å2
2---1.13 Å2-0.16 Å2
3----0.24 Å2
Refinement stepCycle: LAST / Resolution: 2.8→25.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6457 0 40 0 6497
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226667
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.969006
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.995771
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63622.662293
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.528151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0091542
X-RAY DIFFRACTIONr_chiral_restr0.0950.2957
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024898
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.240.23199
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3180.24483
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2229
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2520.2117
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2510.27
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7831.53944
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30126290
X-RAY DIFFRACTIONr_scbond_it1.51333137
X-RAY DIFFRACTIONr_scangle_it2.1924.52716
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.331 57 -
Rwork0.236 1155 -
obs--83.36 %

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