[English] 日本語
Yorodumi
- PDB-6en1: Structure of the Tn1549 transposon Integrase (aa 82-397, R225K) i... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6en1
TitleStructure of the Tn1549 transposon Integrase (aa 82-397, R225K) in complex with a circular intermediate DNA (CI6a-DNA)
Components
  • (DNA (45-MER)) x 2
  • Int protein
KeywordsRECOMBINATION / transposase protein - DNA complex / tyrosine recombinase / Y-transposase / Tn916-like conjugative transposon / antibiotic resistance transfer
Function / homology
Function and homology information


integrase activity / DNA recombination / DNA binding
Similarity search - Function
Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily ...Integrase, Tn916-type, N-terminal DNA binding / DNA binding domain of tn916 integrase / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal / Integrase-like, catalytic domain superfamily / DNA breaking-rejoining enzyme, catalytic core / DNA-binding domain superfamily
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / Int protein
Similarity search - Component
Biological speciesEnterococcus faecalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsRubio-Cosials, A. / Barabas, O.
CitationJournal: Cell / Year: 2018
Title: Transposase-DNA Complex Structures Reveal Mechanisms for Conjugative Transposition of Antibiotic Resistance.
Authors: Rubio-Cosials, A. / Schulz, E.C. / Lambertsen, L. / Smyshlyaev, G. / Rojas-Cordova, C. / Forslund, K. / Karaca, E. / Bebel, A. / Bork, P. / Barabas, O.
History
DepositionOct 4, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Int protein
C: DNA (45-MER)
D: DNA (45-MER)
B: Int protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,4246
Polymers100,2114
Non-polymers2122
Water2,360131
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: SAXS, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-108 kcal/mol
Surface area37880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.740, 123.880, 77.750
Angle α, β, γ (deg.)90.000, 118.210, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Int protein / Integrase


Mass: 36258.668 Da / Num. of mol.: 2 / Mutation: R225K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterococcus faecalis (bacteria) / Gene: int / Plasmid: pETM28 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): pLysS / References: UniProt: Q7BP35
#2: DNA chain DNA (45-MER)


Mass: 13877.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Circular intermediate DNA / Source: (synth.) Enterococcus faecalis (bacteria)
#3: DNA chain DNA (45-MER)


Mass: 13815.955 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Circular intermediate DNA with 6 bp at the crossover region (CI6a: gaaaat)
Source: (synth.) Enterococcus faecalis (bacteria)
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.42 Å3/Da / Density % sol: 64.08 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.1M Na Acetate pH4.6, 30% PEG300

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.6→45.392 Å / Num. obs: 39879 / % possible obs: 99.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 55.71 Å2 / CC1/2: 0.994 / Rrim(I) all: 0.156 / Rsym value: 0.133 / Net I/σ(I): 8.19
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 3.8 % / Mean I/σ(I) obs: 1.02 / Num. unique obs: 10875 / CC1/2: 0.492 / Rrim(I) all: 1.523 / Rsym value: 1.3 / % possible all: 97.2

-
Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XSCALEdata scaling
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6EMY
Resolution: 2.67→45.392 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.24
RfactorNum. reflection% reflection
Rfree0.2436 1868 5.08 %
Rwork0.1881 --
obs0.191 36788 99.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 195.25 Å2 / Biso mean: 65.2466 Å2 / Biso min: 19.88 Å2
Refinement stepCycle: final / Resolution: 2.67→45.392 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4913 1545 34 131 6623
Biso mean--84.98 45.12 -
Num. residues----710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046751
X-RAY DIFFRACTIONf_angle_d0.5949451
X-RAY DIFFRACTIONf_chiral_restr0.0351056
X-RAY DIFFRACTIONf_plane_restr0.004958
X-RAY DIFFRACTIONf_dihedral_angle_d17.5513780
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.67-2.74220.33531460.286226602806100
2.7422-2.82290.32351370.263926542791100
2.8229-2.9140.34261470.278126922839100
2.914-3.01810.3661590.276326582817100
3.0181-3.13890.36211360.275727192855100
3.1389-3.28170.32091300.23526402770100
3.2817-3.45470.27971450.210126892834100
3.4547-3.6710.2461430.186826972840100
3.671-3.95430.23541430.167926952838100
3.9543-4.3520.21631380.151826892827100
4.352-4.98110.2071490.139927012850100
4.9811-6.2730.19211400.164226992839100
6.273-45.39860.18911550.16442727288299
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.3418-0.73560.81632.3727-0.84793.21690.0061-0.2102-0.1983-0.1337-0.1328-0.21120.23140.15190.00010.39170.00490.04980.43140.07530.3546-82.7189-15.969388.9108
21.70190.061-0.28571.3661-0.31291.56750.08530.4119-0.1207-0.3318-0.00540.49760.2873-0.1048-0.00020.5104-0.0929-0.0950.4193-0.02760.5047-106.8687-9.362563.0215
3-0.1514-0.53180.08982.46550.7312.9340.05370.00110.0656-0.3003-0.04620.0436-0.15690.1575-00.3364-0.0094-0.02580.3469-0.0110.3387-97.94774.672363.7563
40.1809-0.9487-1.18090.01542.13370.00630.31770.1133-0.5697-0.2195-0.27950.2928-0.057-0.2024-0.03060.45160.041-0.01860.4596-0.03790.4835-93.6109-18.168956.2747
5-0.00310.005-0.00490.0815-0.15690.25420.1117-1.19781.47250.4073-0.68790.0025-0.1826-0.4082-0.01851.5167-0.22490.50171.2146-0.48191.5867-125.9557-0.643182.4057
60.39790.67021.15711.66941.33272.0669-0.04170.25710.25750.24020.0069-0.18710.0385-0.07920.00070.441-0.00460.13310.49250.07150.4017-96.0258-6.032476.8376
71.24830.10171.15180.5022-0.68191.5907-0.1064-0.17530.4272-0.00770.04060.0605-0.4023-0.018500.4213-0.0320.0290.4915-0.020.4479-62.9774-29.181761.1445
82.4513-1.8151-2.0391.03091.25971.75620.6769-0.060.603-1.41980.1504-1.03690.95040.66290.63911.18730.22960.04710.80870.09610.9595-44.9637-41.720438.8029
90.2549-0.02540.2640.0037-0.02590.2951-0.6432-0.5930.6919-0.7889-0.3054-1.14840.17530.6847-0.02710.94880.15580.37771.15420.54462.1223-39.2061-38.98630.1829
100.841-0.78520.7431.6876-1.39591.03670.22150.17240.31420.1929-0.1465-0.28160.2802-0.173-0.00030.3809-0.01650.04780.4172-0.02240.497-58.5813-32.673455.3359
112.13040.41781.24712.91880.3641.0295-0.8249-0.05570.21190.42350.03310.76890.0468-0.2037-0.47240.4527-0.06080.05920.4601-0.11050.4955-107.0263-2.018279.0413
121.36420.16130.03712.52480.94123.06610.0463-0.20680.25780.0752-0.07370.0116-0.26230.116-00.3554-0.0441-0.01990.4242-0.05520.3981-54.3072-23.566771.9899
131.33530.15180.22120.95070.08531.5473-0.07790.17760.113-0.37730.01270.107-0.2338-0.29430.00030.5751-0.0089-0.06580.3640.05160.3864-65.6273-30.028738.4859
141.5826-1.1051.4660.7799-0.38110.9582-0.1315-0.38210.1213-0.023-0.0740.3276-0.0137-0.31240.00010.32720.0078-0.0230.4337-0.01290.4265-73.5754-43.437751.9228
152.0562-0.03490.80952.87120.43320.53030.17240.1925-0.1117-0.3216-0.01630.06040.12560.0215-0.00010.35160.0099-0.01230.3936-0.00220.3139-65.6161-44.864741.9526
160.521-3.0331-0.65170.39790.3774-0.56910.3701-0.0717-0.1842-0.3718-0.17130.101-0.54110.03810.05640.55520.03930.01780.4564-0.03010.4107-77.8388-21.184646.8327
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 81 through 179 )A81 - 179
2X-RAY DIFFRACTION2chain 'A' and (resid 180 through 222 )A180 - 222
3X-RAY DIFFRACTION3chain 'A' and (resid 223 through 332 )A223 - 332
4X-RAY DIFFRACTION4chain 'A' and (resid 333 through 396 )A333 - 396
5X-RAY DIFFRACTION5chain 'C' and (resid -17 through -13 )C-17 - -13
6X-RAY DIFFRACTION6chain 'C' and (resid -12 through 2 )C-12 - 2
7X-RAY DIFFRACTION7chain 'C' and (resid 3 through 12 )C3 - 12
8X-RAY DIFFRACTION8chain 'C' and (resid 13 through 22 )C13 - 22
9X-RAY DIFFRACTION9chain 'D' and (resid -17 through -13 )D-17 - -13
10X-RAY DIFFRACTION10chain 'D' and (resid -12 through 5 )D-12 - 5
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 23 )D6 - 23
12X-RAY DIFFRACTION12chain 'B' and (resid 81 through 179 )B81 - 179
13X-RAY DIFFRACTION13chain 'B' and (resid 180 through 222 )B180 - 222
14X-RAY DIFFRACTION14chain 'B' and (resid 223 through 275 )B223 - 275
15X-RAY DIFFRACTION15chain 'B' and (resid 276 through 332 )B276 - 332
16X-RAY DIFFRACTION16chain 'B' and (resid 333 through 396 )B333 - 396

+
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