[English] 日本語
Yorodumi
- PDB-4a8e: The structure of a dimeric Xer recombinase from archaea -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4a8e
TitleThe structure of a dimeric Xer recombinase from archaea
ComponentsPROBABLE TYROSINE RECOMBINASE XERC-LIKE
KeywordsCELL CYCLE / CHROMOSOME DIMER RESOLUTION / PAB0255
Function / homology
Function and homology information


tyrosine-based site-specific recombinase activity / DNA transposition / DNA binding / cytoplasm
Similarity search - Function
Tyrosine recombinase XerA / : / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. ...Tyrosine recombinase XerA / : / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / Intergrase catalytic core / Tyrosine recombinase, N-terminal domain / hpI Integrase; Chain A / 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 polymerase; domain 1 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Tyrosine recombinase XerA
Similarity search - Component
Biological speciesPYROCOCCUS ABYSSI (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.99 Å
AuthorsBrooks, M.A. / ElArnaout, T. / Duranda, D. / Lisboa, J. / Lazar, N. / Raynal, B. / vanTilbeurgh, H. / Serre, M. / Quevillon-Cheruel, S.
CitationJournal: Plos One / Year: 2013
Title: The Carboxy-Terminal Alpha N Helix of the Archaeal Xera Tyrosine Recombinase is a Molecular Switch to Control Site-Specific Recombination.
Authors: Serre, M.C. / El Arnaout, T. / Brooks, M.A. / Durand, D. / Lisboa, J. / Lazar, N. / Raynal, B. / Van Tilbeurgh, H. / Quevillon-Cheruel, S.
History
DepositionNov 21, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2014Group: Database references
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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: PROBABLE TYROSINE RECOMBINASE XERC-LIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,68510
Polymers33,9151
Non-polymers7709
Water543
1
A: PROBABLE TYROSINE RECOMBINASE XERC-LIKE
hetero molecules

A: PROBABLE TYROSINE RECOMBINASE XERC-LIKE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,37020
Polymers67,8312
Non-polymers1,54018
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x+1/2,-y+1/2,z1
Buried area5630 Å2
ΔGint-209.2 kcal/mol
Surface area28720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.670, 157.290, 45.550
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-1287-

CL

-
Components

#1: Protein PROBABLE TYROSINE RECOMBINASE XERC-LIKE / XER A


Mass: 33915.262 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PYROCOCCUS ABYSSI (archaea) / Strain: GE5 / ORSAY / Plasmid: PET9 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA PLYS / References: UniProt: Q9V1P5
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 2.7 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.15
Details: 1.8 M AMMONIUM SULFATE, 0.1 M HEPES PH 7.15, 5% (V/V) ETHYLENE GLYCOL.

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8726
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 16, 2004 / Details: TOROIDAL MIRROR
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 6939 / % possible obs: 98.7 % / Observed criterion σ(I): -3 / Redundancy: 4.33 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 3→3.2 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2.38 / % possible all: 97.1

-
Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-TERMINAL DOMAIN OF PAB0255, FOLLOWED BY PDB ENTRY 1A0P

1a0p


Resolution: 2.99→29.81 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.862 / SU B: 19.405 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.29342 341 4.9 %RANDOM
Rwork0.20705 ---
obs0.21111 6598 98.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.624 Å2
Baniso -1Baniso -2Baniso -3
1-1.54 Å20 Å20 Å2
2--0.64 Å20 Å2
3----2.18 Å2
Refinement stepCycle: LAST / Resolution: 2.99→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2143 0 40 3 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0192209
X-RAY DIFFRACTIONr_bond_other_d0.0020.022240
X-RAY DIFFRACTIONr_angle_refined_deg1.4062.0072967
X-RAY DIFFRACTIONr_angle_other_deg0.77835095
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.125264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.43422.47393
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.1115432
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4731521
X-RAY DIFFRACTIONr_chiral_restr0.070.2338
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022360
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.991→3.068 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 17 -
Rwork0.261 369 -
obs--92.57 %

+
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