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- PDB-3hot: Crystal structure of the Mos1 mariner paired end complex with Mn -

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Basic information

Entry
Database: PDB / ID: 3hot
TitleCrystal structure of the Mos1 mariner paired end complex with Mn
Components
  • Mos1 NTS inverted repeat DNA
  • Mos1 TS inverted repeat DNA
  • Transposable element mariner, complete cds
KeywordsTRANSFERASE / DNA BINDING PROTEIN/DNA / protein-DNA complex / synaptic complex / transposase / inverted repeat DNA / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining ...mitotic DNA integrity checkpoint signaling / DNA topoisomerase binding / single-stranded DNA endodeoxyribonuclease activity / histone H3K36 methyltransferase activity / DNA double-strand break processing / histone H3K4 methyltransferase activity / replication fork processing / condensed chromosome / DNA integration / double-strand break repair via nonhomologous end joining / site of double-strand break / single-stranded DNA binding / double-stranded DNA binding / DNA recombination / Hydrolases; Acting on ester bonds / nucleus / metal ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A ...Arc Repressor Mutant, subunit A - #1450 / Transposase, type 1 / Mos1 transposase, HTH domain / : / Transposase (partial DDE domain) / HTH domain in Mos1 transposase / Ribonuclease H-like superfamily/Ribonuclease H / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Mariner Mos1 transposase
Similarity search - Component
Biological speciesDrosophila mauritiana (fry)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.25 Å
AuthorsRichardson, J.M. / Walkinshaw, M.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2009
Title: Molecular architecture of the Mos1 paired-end complex: the structural basis of DNA transposition in a eukaryote
Authors: Richardson, J.M. / Colloms, S.D. / Finnegan, D.J. / Walkinshaw, M.D.
History
DepositionJun 3, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 16, 2013Group: Derived calculations
Revision 1.3Dec 25, 2019Group: Data collection / Derived calculations / Source and taxonomy
Category: ndb_struct_conf_na / ndb_struct_na_base_pair ...ndb_struct_conf_na / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_entity_src_syn / pdbx_struct_conn_angle / reflns / struct_conn / struct_conn_type
Item: _pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id ..._pdbx_entity_src_syn.details / _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific / _reflns.pdbx_Rmerge_I_obs
Revision 1.4Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_conn_type / 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 / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transposable element mariner, complete cds
B: Transposable element mariner, complete cds
C: Mos1 NTS inverted repeat DNA
D: Mos1 TS inverted repeat DNA
E: Mos1 NTS inverted repeat DNA
F: Mos1 TS inverted repeat DNA
G: Mos1 NTS inverted repeat DNA
H: Mos1 TS inverted repeat DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,21511
Polymers130,9688
Non-polymers2473
Water543
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area28690 Å2
ΔGint-134 kcal/mol
Surface area54560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.294, 84.989, 132.116
Angle α, β, γ (deg.)90.00, 99.21, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transposable element mariner, complete cds / Mos1 transposase


Mass: 40865.316 Da / Num. of mol.: 2 / Mutation: T216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila mauritiana (fry) / Production host: Escherichia coli (E. coli)
References: UniProt: Q7JQ07, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 6 molecules CEGDFH

#2: DNA chain Mos1 NTS inverted repeat DNA


Mass: 7879.900 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain Mos1 TS inverted repeat DNA


Mass: 8532.542 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 6 molecules

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


Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Sequence detailsTHESE RESIDUES WERE BASED ON THE NUCLEOTIDE SEQUENCE EMBL:X78906.

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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: 5.0901 Å3/Da / Density % sol: 75.8355 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 17, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3.25→40 Å / Num. all: 38972 / Num. obs: 38972 / % possible obs: 93.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.2 % / Rmerge(I) obs: 0.173 / Net I/σ(I): 8.2
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.5 / % possible all: 97.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2F7T

2f7t


Resolution: 3.25→38.87 Å / Cor.coef. Fo:Fc: 0.87 / Cor.coef. Fo:Fc free: 0.814 / Occupancy max: 1 / Occupancy min: 1 / SU B: 66.747 / SU ML: 0.47 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 2.175 / ESU R Free: 0.506 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30413 1970 5.1 %RANDOM
Rwork0.24781 ---
obs0.25062 36970 93.17 %-
all-38940 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.926 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20 Å2-3.87 Å2
2--3.95 Å20 Å2
3----5.32 Å2
Refinement stepCycle: LAST / Resolution: 3.25→38.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5643 3258 11 3 8915
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0219447
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7042.38213455
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075672
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.39223.365312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.923151037
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.31554
X-RAY DIFFRACTIONr_chiral_restr0.1020.21426
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216158
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5221.53384
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.00325457
X-RAY DIFFRACTIONr_scbond_it1.14236063
X-RAY DIFFRACTIONr_scangle_it1.9954.57998
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.25→3.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.364 145 -
Rwork0.338 2790 -
obs--97.35 %
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)
10.71020.13480.10990.6919-0.07170.74810.14550.0266-0.0283-0.0014-0.0923-0.0284-0.06-0.0282-0.05320.04450.0236-0.00210.0416-0.00450.0129.4765-10.9686-3.0177
20.7752-1.10912.48231.9972-3.90728.81440.22310.5534-0.120.073-0.24490.103-0.20811.88890.02180.90810.0209-0.2951.57260.12450.224942.9149-29.802164.7664
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 345
2X-RAY DIFFRACTION1B5 - 345
3X-RAY DIFFRACTION1C4 - 28
4X-RAY DIFFRACTION1D29 - 56
5X-RAY DIFFRACTION1E4 - 28
6X-RAY DIFFRACTION1F29 - 56
7X-RAY DIFFRACTION2G4 - 28
8X-RAY DIFFRACTION2H29 - 56

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