[English] 日本語
Yorodumi
- PDB-4fcy: Crystal structure of the bacteriophage Mu transpososome -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fcy
TitleCrystal structure of the bacteriophage Mu transpososome
Components
  • DNA (13-MER)
  • DNA (49-MER)
  • DNA (68-MER)
  • Transposase
KeywordsDNA BINDING PROTEIN/DNA / RNaseH / DDE transposase / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication ...Ligases; Forming phosphoric-ester bonds / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 3'-phosphomonoesters / latency-replication decision / transposase activity / DNA transposition / double-stranded DNA endonuclease activity / viral DNA genome replication / ligase activity / DNA integration / DNA replication / host cell cytoplasm / DNA repair / DNA binding / metal ion binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2550 / Transposase, Mu, C-terminal / Bacteriophage Mu, transposase / Mu DNA binding, I gamma subdomain / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Transposase, Mu, C-terminal ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2550 / Transposase, Mu, C-terminal / Bacteriophage Mu, transposase / Mu DNA binding, I gamma subdomain / Bacteriophage Mu transposase / Mu DNA binding, I gamma subdomain / Mu-type HTH domain / Mu DNA-binding domain / Mu-type HTH domain profile. / Transposase, Mu, C-terminal / Transposase-like, Mu, C-terminal / Mu transposase, C-terminal / Putative DNA-binding domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Homeodomain-like / Ribonuclease H-like superfamily/Ribonuclease H / Helix non-globular / Homeobox-like domain superfamily / Special / SH3 type barrels. / Nucleotidyltransferase; domain 5 / Arc Repressor Mutant, subunit A / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Roll / Winged helix-like DNA-binding domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / DDE-recombinase A
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIRAS / Resolution: 3.706 Å
AuthorsMontano, S.P. / Pigli, Y.Z. / Rice, P.A.
CitationJournal: Nature / Year: 2012
Title: The Mu transpososome structure sheds light on DDE recombinase evolution.
Authors: Montano, S.P. / Pigli, Y.Z. / Rice, P.A.
History
DepositionMay 25, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)


Theoretical massNumber of molelcules
Total (without water)160,0955
Polymers160,0955
Non-polymers00
Water00
1
A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)

A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)


Theoretical massNumber of molelcules
Total (without water)320,19010
Polymers320,19010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_655-x+1,-y,z1
Buried area35630 Å2
ΔGint-208 kcal/mol
Surface area141140 Å2
MethodPISA
2
A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)

A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)

A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)

A: Transposase
B: Transposase
C: DNA (68-MER)
E: DNA (13-MER)
D: DNA (49-MER)


Theoretical massNumber of molelcules
Total (without water)640,38120
Polymers640,38120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_545y+1/2,x-1/2,-z+1/21
crystal symmetry operation10_655-x+1,-y,z1
crystal symmetry operation16_555-y+1/2,-x+1/2,-z+1/21
Buried area76450 Å2
ΔGint-432 kcal/mol
Surface area277090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.138, 196.138, 349.980
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23
14
24

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-ID
111chain 'B' and (resseq 258:272 or resseq 276:285 or resseq...B
211chain 'A' and (resseq 258:272 or resseq 276:285 or resseq...A
112chain 'B' and (resseq 180:184 or resseq 188:189 or resseq 208:212 )B
212chain 'A' and (resseq 180:184 or resseq 188:189 or resseq 208:212 )A
113chain 'B' and (resseq 491:504 or resseq 508:545 or resseq 555:560 )B
213chain 'A' and (resseq 491:504 or resseq 508:545 or resseq 555:560 )A
114chain 'B' and (resseq 89:95 or resseq 99:101 or resseq...B
214chain 'A' and (resseq 89:95 or resseq 99:101 or resseq...A

NCS ensembles :
ID
1
2
3
4

-
Components

#1: Protein Transposase


Mass: 60034.254 Da / Num. of mol.: 2 / Fragment: UNP residues 77-605 / Mutation: M521L, N525L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Gene: A, 3 / Production host: Escherichia coli (E. coli) / References: UniProt: P07636
#2: DNA chain DNA (68-MER)


Mass: 20912.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage Mu (virus)
#3: DNA chain DNA (13-MER)


Mass: 3913.591 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage Mu (virus)
#4: DNA chain DNA (49-MER)


Mass: 15200.815 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage Mu (virus)

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 5.26 Å3/Da / Density % sol: 76.6 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 24-28% PEG400, 0.2 M magnesium chloride, 0.1 M HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 17160 / % possible obs: 99.7 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3
Reflection shellResolution: 3.5→3.56 Å / % possible all: 97.2

-
Processing

Software
NameVersionClassification
HKL-3000data collection
MLPHAREphasing
PHENIX(phenix.refine: dev_847)refinement
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 3.706→49.035 Å / SU ML: 2.1 / σ(F): 0 / Phase error: 62.1 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.4374 859 5.01 %RANDOM
Rwork0.3928 ---
obs0.3951 17160 46.95 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 171.708 Å2 / ksol: 0.321 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.7274 Å20 Å2-0 Å2
2--6.7274 Å2-0 Å2
3----13.4548 Å2
Refinement stepCycle: LAST / Resolution: 3.706→49.035 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7397 2659 0 0 10056
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610541
X-RAY DIFFRACTIONf_angle_d1.17414787
X-RAY DIFFRACTIONf_dihedral_angle_d22.574082
X-RAY DIFFRACTIONf_chiral_restr0.0761590
X-RAY DIFFRACTIONf_plane_restr0.0051445
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1108X-RAY DIFFRACTIONPOSITIONAL
12A1108X-RAY DIFFRACTIONPOSITIONAL0.012
21B95X-RAY DIFFRACTIONPOSITIONAL
22A95X-RAY DIFFRACTIONPOSITIONAL0.018
31B441X-RAY DIFFRACTIONPOSITIONAL
32A441X-RAY DIFFRACTIONPOSITIONAL0.012
41B479X-RAY DIFFRACTIONPOSITIONAL
42A479X-RAY DIFFRACTIONPOSITIONAL0.013
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7059-3.9380.6374100.614212X-RAY DIFFRACTION4
3.938-4.24190.5489230.5716603X-RAY DIFFRACTION10
4.2419-4.66840.5692740.54461360X-RAY DIFFRACTION24
4.6684-5.34330.52481540.52653031X-RAY DIFFRACTION53
5.3433-6.72920.51012950.50565204X-RAY DIFFRACTION90
6.7292-49.03880.37973030.31215891X-RAY DIFFRACTION98
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)
11.86640.85721.98071.66121.5652.31460.81820.0153-1.41360.22952.11630.5875-0.4017-0.54831.26162.51770.41660.53951.09280.83922.233360.877362.2382111.5529
21.57040.4077-0.47520.05290.07870.91911.42410.7073-0.2182-0.6317-0.3945-0.4257-0.866-0.31362.5471.71760.39521.41910.9485-2.87440.100868.619255.452170.9739
36.8995-2.3063-0.58071.0486-0.76544.12420.00580.08833.5420.11450.038-1.0984-0.87033.8735-0.07191.9603-0.46910.07691.708-0.14720.648787.353231.849955.128
40.4804-1.0343-0.26763.57880.97131.06130.09710.4292.514-2.6018-0.67053.4085-0.188-1.0101-1.6023-3.21763.89742.9038-1.8889-1.0139-1.040699.079720.212515.3041
52.3712-0.6035-0.26275.0906-0.5847.28711.29150.0562-0.8747-0.89630.43942.17231.8696-1.66716.41290.14710.59580.02550.9157-1.02440.427464.69927.340945.8288
60.09940.1701-0.44040.5939-1.40992.621-0.08451.1168-0.1851-1.1484-0.76440.2913-1.18150.3268-1.73042.84951.4567-1.38132.391-0.14970.111774.2993-13.6233-5.1528
74.29490.0292-1.42211.036-1.50482.6064-1.41861.33892.04370.15470.82470.2569-1.5894-1.25713.67673.08850.8369-2.51742.4769-0.93822.915462.7944-11.7505-33.4214
84.75613.3739-0.3933.8563-0.03511.1058-0.96112.44711.0026-1.1366-0.685-0.70060.9832-0.5967-6.3054.03242.4727-1.24041.60330.83720.757982.316210.0665-29.6552
90.9140.4716-0.17520.54250.83012.47630.27810.701-1.2078-0.0473-0.80911.47860.1962-0.87780.94771.91761.78651.1791.09530.08822.397796.3397-6.3345-30.6158
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'C' and ((resseq 2:17))) or (chain 'B' and ((resseq 88:165))) or (chain 'D' and ((resseq 41:54)))
2X-RAY DIFFRACTION2(chain 'C' and ((resseq 18:25))) or (chain 'B' and ((resseq 178:242))) or (chain 'D' and ((resseq 31:40)))
3X-RAY DIFFRACTION3(chain 'A' and ((resseq 88:165))) or (chain 'C' and ((resseq 26:38))) or (chain 'D' and ((resseq 20:30)))
4X-RAY DIFFRACTION4(chain 'A' and ((resseq 178:247))) or (chain 'C' and ((resseq 39:51))) or (chain 'B' and ((resseq 568:605))) or (chain 'D' and ((resseq 7:19)))
5X-RAY DIFFRACTION5chain 'B' and ((resseq 258:560))
6X-RAY DIFFRACTION6(chain 'A' and ((resseq 258:489)))
7X-RAY DIFFRACTION7chain 'A' and ((resseq 491:560))
8X-RAY DIFFRACTION8(chain 'C' and ((resseq 52:69))) or (chain 'E' and ((resseq 2:14)))
9X-RAY DIFFRACTION9chain 'A' and ((resseq 572:594))

+
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://pdbjlvh1.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