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- PDB-4dm0: TN5 transposase: 20MER OUTSIDE END 2 MN complex -

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Basic information

Entry
Database: PDB / ID: 4dm0
TitleTN5 transposase: 20MER OUTSIDE END 2 MN complex
Components
  • DNA NON-TRANSFERRED STRAND
  • DNA TRANSFERRED STRAND
  • Transposase for transposon Tn5
KeywordsHYDROLASE/DNA / TRANSPOSASE / RIBONUCLEASE H-LIKE MOTIF / PROTEIN-DNA COMPLEX / SYNAPTIC COMPLEX / DNA RECOMBINATION-DNA COMPLEX / HYDROLASE-DNA complex
Function / homology
Function and homology information


transposase activity / DNA transposition / endonuclease activity / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding
Similarity search - Function
Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : ...Tn5 transposase; domain 1 / Transferase Inhibitor Protein From Tn5; Chain A, domain2 / Transferase Inhibitor Protein From Tn5; Chain / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase Inhibitor Protein From Tn5; Chain A, domain 1 / Transposase, IS4-like / Transposase, Tn5-like, N-terminal / Transposase, Tn5-like, C-terminal / Transposase, Tn5-like, N-terminal domain superfamily / : / Transposase DDE domain / Transposase DNA-binding / Serum Albumin; Chain A, Domain 1 / Ribonuclease H-like superfamily / Alpha-Beta Complex / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Transposase for transposon Tn5
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsKlenchin, V.A. / Lovell, S. / Goryshin, I.Y. / Reznikoff, W.R. / Rayment, I.
CitationJournal: Nat.Struct.Biol. / Year: 2002
Title: Two-metal active site binding of a TN5 transposase synaptic complex
Authors: Lovell, S. / Goryshin, I.Y. / Reznikoff, W.R. / Rayment, I.
History
DepositionFeb 6, 2012Deposition site: RCSB / Processing site: RCSB
SupersessionFeb 22, 2012ID: 1MUR
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.2Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_ref_seq_dif.details / _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 for transposon Tn5
B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1737
Polymers65,9463
Non-polymers2274
Water6,521362
1
A: Transposase for transposon Tn5
B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
hetero molecules

A: Transposase for transposon Tn5
B: DNA TRANSFERRED STRAND
C: DNA NON-TRANSFERRED STRAND
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,34614
Polymers131,8936
Non-polymers4548
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_544x,x-y-1,-z-1/61
Buried area19340 Å2
ΔGint-121 kcal/mol
Surface area46710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.378, 112.378, 232.783
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11A-503-

MN

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Transposase for transposon Tn5 / Tnp


Mass: 53367.113 Da / Num. of mol.: 1 / Mutation: E54K, M56A, E345K, L372P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: tnpA, tnp / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)PLYSS
References: UniProt: Q46731, Hydrolases; Acting on ester bonds

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA TRANSFERRED STRAND


Mass: 6526.246 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE 21 BP SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON
#3: DNA chain DNA NON-TRANSFERRED STRAND


Mass: 6052.943 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: THE 20 BP SEQUENCE OCCURS NATURALLY IN THE TN5 TRANSPOSON

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Non-polymers , 3 types, 366 molecules

#4: Chemical ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.22 Å3/Da / Density % sol: 61.77 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 5
Details: 15% PEG 1500, 0.35M POTASSIUM GLUTAMATE, 0.05M POTASSIUM SUCCINATE, pH 5.0, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97625 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Mar 21, 2001
RadiationMonochromator: UNDULATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 2.5→30 Å / Num. all: 31250 / Num. obs: 31250 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 16.9 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.091 / Χ2: 1.111 / Net I/σ(I): 29.428
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.5-2.5411.70.3896.78615360.835100
2.54-2.5911.90.3437.49115050.791100
2.59-2.64120.3118.60915320.8100
2.64-2.6911.90.2799.5815350.878100
2.69-2.75120.24410.41915250.8100
2.75-2.8211.90.21111.87415260.797100
2.82-2.8911.80.19113.25215320.813100
2.89-2.9611.80.1615.44915390.795100
2.96-3.0511.80.1317.80815420.784100
3.05-3.1511.60.10921.09715310.84100
3.15-3.2617.50.17826.41515371.416100
3.26-3.3922.40.14933.09515521.229100
3.39-3.5522.90.13336.40215571.276100
3.55-3.7323.10.11141.23115541.667100
3.73-3.9722.90.0946.08415591.265100
3.97-4.2722.90.07251.42715821.189100
4.27-4.722.70.0655.71315951.231100
4.7-5.3822.40.05955.5915991.19100
5.38-6.7621.70.0653.75716421.104100
6.76-30200.03566.48417701.06299.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 40.54 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å28.86 Å
Translation2.5 Å28.86 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
d*TREKdata scaling
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1F3I

1f3i
PDB Unreleased entry


Resolution: 2.5→28.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.1855 / WRfactor Rwork: 0.1588 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8706 / SU B: 10.863 / SU ML: 0.13 / SU R Cruickshank DPI: 0.2925 / SU Rfree: 0.2071 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.293 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.2028 1562 5 %RANDOM
Rwork0.17 ---
all0.1717 31328 --
obs0.1717 31103 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 134.61 Å2 / Biso mean: 35.8276 Å2 / Biso min: 8.45 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å20 Å2
3----0.84 Å2
Refinement stepCycle: LAST / Resolution: 2.5→28.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3589 822 7 362 4780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0214589
X-RAY DIFFRACTIONr_angle_refined_deg1.2022.1886373
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.60223.106161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0115652
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2031534
X-RAY DIFFRACTIONr_chiral_restr0.070.2704
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213170
X-RAY DIFFRACTIONr_mcbond_it2.62932286
X-RAY DIFFRACTIONr_mcangle_it4.784303643
X-RAY DIFFRACTIONr_scbond_it5.32952299
X-RAY DIFFRACTIONr_scangle_it7.651502727
LS refinement shellResolution: 2.5→2.554 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 129 -
Rwork0.219 2087 -
all-2216 -
obs--98.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9129-0.4847-0.37040.98880.37560.6868-0.005-0.06780.04980.10580.02650.05860.00040.0443-0.02160.0505-0.04150.0120.067-0.02220.032834.204-36.0492.32
21.5196-0.1932-0.47840.72390.4263.04790.06650.04120.1019-0.1469-0.0970.0866-0.0957-0.45950.03060.06760.00520.04780.0778-0.03660.136715.053-18.947-4.774
32.28850.08020.18641.7460.26181.38250.02850.12250.42970.03510.0156-0.2248-0.44630.1712-0.04410.1883-0.10410.03120.1068-0.00610.14452.606-20.812-16.879
42.2052-0.2404-0.37671.41870.33392.45370.0478-0.1654-0.04440.02430.02150.13920.04080.0102-0.06930.0512-0.01710.01580.0523-0.01120.065827.807-27.382-22.061
52.8167-0.7202-0.35654.3891.42421.16880.51510.23730.2956-1.1304-0.0527-0.0955-0.5603-0.1888-0.46240.50540.04530.16050.11620.12210.258837.712-16.465-49.718
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 228
2X-RAY DIFFRACTION1A323 - 372
3X-RAY DIFFRACTION2A229 - 322
4X-RAY DIFFRACTION3A388 - 477
5X-RAY DIFFRACTION4B111 - 121
6X-RAY DIFFRACTION4C201 - 210
7X-RAY DIFFRACTION5B101 - 110
8X-RAY DIFFRACTION5C211 - 220

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