[English] 日本語
Yorodumi
- PDB-3hot: Crystal structure of the Mos1 mariner paired end complex with Mn -

+
Open data


ID or keywords:

Loading...

-
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


DNA integration / endonuclease activity / DNA recombination / Hydrolases; Acting on ester bonds / DNA binding / metal ion binding / nucleus
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 / Ribonuclease H superfamily ...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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
Components

-
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

-
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)

-
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 / Sulfate


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


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

-
Details

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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more