[English] 日本語
Yorodumi
- PDB-2r0q: Crystal structure of a serine recombinase- DNA regulatory complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2r0q
TitleCrystal structure of a serine recombinase- DNA regulatory complex
Components
  • (31-MER) x 2
  • Putative transposon Tn552 DNA-invertase bin3
KeywordsRECOMBINATION/DNA / site-specific recombinase / resolvase / dna-binding protein / protein-dna complex / DNA integration / DNA invertase / DNA recombination / Plasmid / Transposable element / Transposition / RECOMBINATION-DNA COMPLEX
Function / homology
Function and homology information


transposition / DNA strand exchange activity / DNA integration / DNA binding
Similarity search - Function
Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain ...Resolvase, N-terminal catalytic domain / Site-specific recombinases signature 2. / Resolvase, HTH domain / Helix-turn-helix domain of resolvase / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain / Resolvase-like, N-terminal catalytic domain superfamily / Resolvase, N terminal domain / Resolvase, N terminal domain / Homeodomain-like / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Putative transposon Tn552 DNA-invertase bin3
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.2 Å
AuthorsRice, P.A. / Mouw, K.W.
CitationJournal: Mol.Cell / Year: 2008
Title: Architecture of a serine recombinase-DNA regulatory complex.
Authors: Mouw, K.W. / Rowland, S.J. / Gajjar, M.M. / Boocock, M.R. / Stark, W.M. / Rice, P.A.
History
DepositionAug 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 31-MER
B: 31-MER
G: 31-MER
H: 31-MER
C: Putative transposon Tn552 DNA-invertase bin3
D: Putative transposon Tn552 DNA-invertase bin3
E: Putative transposon Tn552 DNA-invertase bin3
F: Putative transposon Tn552 DNA-invertase bin3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,55310
Polymers135,3618
Non-polymers1922
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24050 Å2
ΔGint-182.7 kcal/mol
Surface area57560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)132.500, 132.500, 315.100
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

-
Components

#1: DNA chain 31-MER


Mass: 9619.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: site ii dna strand 1
#2: DNA chain 31-MER


Mass: 9437.147 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: site ii dna strand 2
#3: Protein
Putative transposon Tn552 DNA-invertase bin3


Mass: 24312.117 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Strain: NCTC 9789 / Gene: bin3 / Plasmid: pSA1122 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) pLysS / References: UniProt: P20384
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 4

-
Sample preparation

CrystalDensity Matthews: 5.898773 Å3/Da / Density % sol: 79.148209 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: drops containing 25 mM TRIS and 100 mM ammonium sulfate were mixed 1:1 with the sin-dna complex solution, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Components of the solutions
IDNameCrystal-IDSol-ID
1TRIS11
2ammonium sulfate11
3H2O11
4TRIS12
5ammonium sulfate12
6H2O12

-
Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID10.91977, 0.91988
SYNCHROTRONAPS 19-ID21.77
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDFeb 8, 2006
ADSC QUANTUM 3152CCDFeb 8, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si 111MADMx-ray1
2Si 111SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.919771
20.919881
31.771
ReflectionResolution: 3.21→50 Å / Num. all: 56885 / Num. obs: 55122 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Redundancy: 7.8 % / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.44
Reflection shellResolution: 3.21→3.34 Å / Redundancy: 7.5 % / Mean I/σ(I) obs: 2.87 / Num. unique all: 5436 / % possible all: 95.6

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 3.2→50 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.291 2407 4.7 %random
Rwork0.267 ---
all-51441 --
obs-48157 93.6 %-
Solvent computationBsol: 10 Å2
Displacement parametersBiso mean: 80.563 Å2
Baniso -1Baniso -2Baniso -3
1--13.197 Å2-11.547 Å20 Å2
2---13.705 Å20 Å2
3---26.902 Å2
Refinement stepCycle: LAST / Resolution: 3.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6160 2530 10 0 8700
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.353
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3ion.param

+
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