[English] 日本語
Yorodumi
- PDB-5hxy: Crystal structure of XerA recombinase -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5hxy
TitleCrystal structure of XerA recombinase
ComponentsTyrosine recombinase XerA
KeywordsRECOMBINATION / recombinase / XerA
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 / : / Phage integrase family / Core-binding (CB) domain / Core-binding (CB) domain profile. / Integrase, catalytic domain / Tyrosine recombinase domain profile. / Integrase/recombinase, N-terminal ...Tyrosine recombinase XerA / Phage integrase, N-terminal SAM-like domain / Integrase, SAM-like, N-terminal / : / 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
Similarity search - Domain/homology
PHOSPHATE ION / Tyrosine recombinase XerA
Similarity search - Component
Biological speciesThermoplasma acidophilum DSM 1728 (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsHwang, K.Y. / Nam, K.H.
Funding support Korea, Republic Of, 2items
OrganizationGrant numberCountry
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1A1A2059440 Korea, Republic Of
National Research Foundation of Korea (NRF) grant funded by the Korea government (MEST)NRF-2014R1212513 Korea, Republic Of
CitationJournal: FEBS Lett. / Year: 2016
Title: Crystal structure of Thermoplasma acidophilum XerA recombinase shows large C-shape clamp conformation and cis-cleavage mode for nucleophilic tyrosine
Authors: Jo, C.H. / Kim, J. / Han, A.R. / Park, S.Y. / Hwang, K.Y. / Nam, K.H.
History
DepositionJan 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tyrosine recombinase XerA
B: Tyrosine recombinase XerA
C: Tyrosine recombinase XerA
D: Tyrosine recombinase XerA
E: Tyrosine recombinase XerA
F: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,70321
Polymers222,2786
Non-polymers1,42515
Water8,845491
1
A: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,4265
Polymers37,0461
Non-polymers3804
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3314
Polymers37,0461
Non-polymers2853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Tyrosine recombinase XerA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2363
Polymers37,0461
Non-polymers1902
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)182.860, 105.968, 115.586
Angle α, β, γ (deg.)90.00, 110.01, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
Tyrosine recombinase XerA / DNA recombinase


Mass: 37046.410 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum DSM 1728 (acidophilic)
Strain: DSM 1728 / Gene: xerA, Ta1314 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9HIM5
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: PO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.04 %
Crystal growTemperature: 295.5 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: PEG 4000, ADA, LiSO4

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-5A / Wavelength: 0.97952, 0.97987, 0.9800
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 3, 2008
RadiationMonochromator: Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979521
20.979871
30.981
ReflectionResolution: 2.5→50 Å / Num. obs: 68638 / % possible obs: 95.4 % / Redundancy: 3.3 % / Net I/σ(I): 13.69

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-2000data collection
HKL-2000data scaling
SOLVEphasing
RESOLVEmodel building
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MAD / Resolution: 2.5→47.66 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.888 / SU B: 9.342 / SU ML: 0.204 / Cross valid method: THROUGHOUT / ESU R: 0.613 / ESU R Free: 0.292 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24321 3479 5.1 %RANDOM
Rwork0.18847 ---
obs0.19129 65159 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.442 Å2
Baniso -1Baniso -2Baniso -3
1--0.57 Å2-0 Å20.25 Å2
2---1.04 Å20 Å2
3---1.2 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13501 0 75 491 14067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.01913793
X-RAY DIFFRACTIONr_bond_other_d0.0010.0213514
X-RAY DIFFRACTIONr_angle_refined_deg1.821.98918576
X-RAY DIFFRACTIONr_angle_other_deg0.862330990
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.17151642
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93122.485648
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.504152459
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.94715148
X-RAY DIFFRACTIONr_chiral_restr0.120.22089
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0215133
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023225
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_it2.2873.1566604
X-RAY DIFFRACTIONr_mcbond_other2.2873.1566603
X-RAY DIFFRACTIONr_mcangle_it3.674.7198234
X-RAY DIFFRACTIONr_mcangle_other3.674.7198235
X-RAY DIFFRACTIONr_scbond_it2.7853.5047189
X-RAY DIFFRACTIONr_scbond_other2.7113.4797130
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3055.08110253
X-RAY DIFFRACTIONr_long_range_B_refined6.525.11816741
X-RAY DIFFRACTIONr_long_range_B_other6.36825.09516658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.497→2.562 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 220 -
Rwork0.267 4228 -
obs--83.88 %

+
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