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- PDB-4d1q: Hermes transposase bound to its terminal inverted repeat -

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Basic information

Entry
Database: PDB / ID: 4d1q
TitleHermes transposase bound to its terminal inverted repeat
Components
  • (TERMINAL INVERTED REPEAT) x 2
  • TRANSPOSASE
KeywordsPROTEIN-DNA COMPLEX / TRANSPOSITION / TRANPOSOSOME / HAT
Function / homology
Function and homology information


nucleic acid metabolic process / protein dimerization activity / regulation of transcription by RNA polymerase II / DNA binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
Zinc finger, BED domain-containing / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily ...Zinc finger, BED domain-containing / Hermes trasposase, DNA-binding domain / Hermes transposase DNA-binding domain / HAT, C-terminal dimerisation domain / hAT family C-terminal dimerisation region / BED zinc finger / Zinc finger, BED-type / Zinc finger BED-type profile. / Arc Repressor Mutant, subunit A / Ribonuclease H-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Transposase
Similarity search - Component
Biological speciesMUSCA DOMESTICA (house fly)
MethodX-RAY DIFFRACTION / SIRAS / Resolution: 3.4 Å
AuthorsHickman, A.B. / Ewis, H. / Li, X. / Knapp, J. / Laver, T. / Doss, A.L. / Tolun, G. / Steven, A. / Grishaev, A. / Bax, A. ...Hickman, A.B. / Ewis, H. / Li, X. / Knapp, J. / Laver, T. / Doss, A.L. / Tolun, G. / Steven, A. / Grishaev, A. / Bax, A. / Atkinson, P. / Craig, N.L. / Dyda, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2014
Title: Structural Basis of Hat Transposon End Recognition by Hermes, an Octameric DNA Transposase from Musca Domestica.
Authors: Hickman, A.B. / Ewis, H.E. / Li, X. / Knapp, J.A. / Laver, T. / Doss, A. / Tolun, G. / Steven, A.C. / Grishaev, A. / Bax, A. / Atkinson, P.W. / Craig, N.L. / Dyda, F.
History
DepositionMay 4, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 30, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 28, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.2May 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.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_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: TERMINAL INVERTED REPEAT
D: TERMINAL INVERTED REPEAT
E: TERMINAL INVERTED REPEAT
F: TERMINAL INVERTED REPEAT
G: TRANSPOSASE
H: TRANSPOSASE
I: TERMINAL INVERTED REPEAT
J: TERMINAL INVERTED REPEAT
K: TERMINAL INVERTED REPEAT
L: TERMINAL INVERTED REPEAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)283,37716
Polymers283,28512
Non-polymers924
Water00
1
A: TRANSPOSASE
B: TRANSPOSASE
C: TERMINAL INVERTED REPEAT
D: TERMINAL INVERTED REPEAT
E: TERMINAL INVERTED REPEAT
F: TERMINAL INVERTED REPEAT
G: TRANSPOSASE
H: TRANSPOSASE
I: TERMINAL INVERTED REPEAT
J: TERMINAL INVERTED REPEAT
K: TERMINAL INVERTED REPEAT
L: TERMINAL INVERTED REPEAT
hetero molecules

A: TRANSPOSASE
B: TRANSPOSASE
C: TERMINAL INVERTED REPEAT
D: TERMINAL INVERTED REPEAT
E: TERMINAL INVERTED REPEAT
F: TERMINAL INVERTED REPEAT
G: TRANSPOSASE
H: TRANSPOSASE
I: TERMINAL INVERTED REPEAT
J: TERMINAL INVERTED REPEAT
K: TERMINAL INVERTED REPEAT
L: TERMINAL INVERTED REPEAT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)566,75532
Polymers566,57124
Non-polymers1848
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area81040 Å2
ΔGint-414.3 kcal/mol
Surface area249780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)265.150, 265.150, 157.640
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3568, 0.3738, -0.8561), (0.3715, -0.7841, -0.4972), (-0.8571, -0.4954, 0.1409)-0.0212, 104.0301, 45.2756
2given(0.597, -0.5588, 0.5757), (0.727, 0.0734, -0.6827), (0.3392, 0.8261, 0.45)32.1908, 29.8965, -109.5865
3given(-0.239, -0.4986, -0.8332), (-0.5101, -0.6657, 0.5447), (-0.8263, 0.5552, -0.0952)95.715, 145.0766, -11.8756

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Components

#1: Protein
TRANSPOSASE / HERMES TRANSPOSASE


Mass: 61316.133 Da / Num. of mol.: 4
Fragment: DIMERIZATION, CATALYTIC AND INSERTION DOMAINS, RESDIUES 79-612
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUSCA DOMESTICA (house fly) / Plasmid: PBAD/MYC-HIS / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TOP10 / References: UniProt: Q25442
#2: DNA chain
TERMINAL INVERTED REPEAT


Mass: 4613.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) MUSCA DOMESTICA (house fly)
#3: DNA chain
TERMINAL INVERTED REPEAT


Mass: 4892.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) MUSCA DOMESTICA (house fly)
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
Nonpolymer detailsSODIUM ION (NA): SODIUM IONS
Sequence detailsMOBILE ELEMENT

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 6.1 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 6.5
Details: 3 UL OF THE HERMES 79-612/L16-1T COMPLEX AT 8 MG/ML PROTEIN WAS MIXED WITH 1 UL WELL SOLUTION CONSISTING OF 0.18 M KCL, 5 MM DTT, 0.8 M K, NA TARTRATE, 0.1 M MES PH 6.5, AND 5% (V/V) T-BUTANOL.

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418
DetectorType: RIGAKU IMAGING PLATE / Date: Feb 17, 2011 / Details: MULTILAYER MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. obs: 94693 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 13.13 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 12.54

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
SHARPphasing
DMphasing
CNS1.3refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 3.4→30 Å / Rfactor Rfree error: 0.009 / 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
Rfree0.2543 870 1 %RANDOM
Rwork0.2118 ---
obs0.2118 86915 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 29.5451 Å2 / ksol: 0.28 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.96 Å20 Å20 Å2
2---1.96 Å20 Å2
3---3.92 Å2
Refinement stepCycle: LAST / Resolution: 3.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16209 2524 4 0 18737
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.016
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
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.PARAMTOPHCSDX.PRO,DNA-RNA.TOP

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