[English] 日本語
Yorodumi
- PDB-5udo: Crystal structure of the coiled-coil domain from Listeria Innocua... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5udo
TitleCrystal structure of the coiled-coil domain from Listeria Innocua Phage Integrase (Tetragonal Form II)
ComponentsA118 serine integrase
KeywordsRECOMBINATION / site-specific recombination / coiled-coil
Function / homology
Function and homology information


DNA strand exchange activity / DNA integration / DNA binding / metal ion binding
Similarity search - Function
Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / Recombinase, conserved site / Site-specific recombinases active site. / Resolvase/invertase-type recombinase catalytic domain profile. / Resolvase, N-terminal catalytic domain ...Recombinase zinc beta ribbon domain / Recombinase / Recombinase zinc beta ribbon domain / DNA-binding recombinase domain / DNA-binding recombinase domain superfamily / DNA-binding recombinase domain profile. / 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
Similarity search - Domain/homology
Integrase [Bacteriophage A118]
Similarity search - Component
Biological speciesListeria innocua (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.541 Å
AuthorsGupta, K. / Yuan, J.B. / Sharp, R. / Van Duyne, G.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5 R01 GM108751 03 United States
Citation
Journal: Nucleic Acids Res. / Year: 2017
Title: Coiled-coil interactions mediate serine integrase directionality.
Authors: Gupta, K. / Sharp, R. / Yuan, J.B. / Li, H. / Van Duyne, G.D.
#1: Journal: Nucleic Acids Res. / Year: 2013
Title: Attachment site recognition and regulation of directionality by the serine integrases.
Authors: Rutherford, K. / Yuan, P. / Perry, K. / Sharp, R. / Van Duyne, G.D.
History
DepositionDec 28, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_high

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: A118 serine integrase
B: A118 serine integrase
C: A118 serine integrase
D: A118 serine integrase
E: A118 serine integrase
F: A118 serine integrase
G: A118 serine integrase
H: A118 serine integrase


Theoretical massNumber of molelcules
Total (without water)313,2458
Polymers313,2458
Non-polymers00
Water14,034779
1
A: A118 serine integrase
B: A118 serine integrase


Theoretical massNumber of molelcules
Total (without water)78,3112
Polymers78,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area6800 Å2
MethodPISA
2
C: A118 serine integrase
D: A118 serine integrase


Theoretical massNumber of molelcules
Total (without water)78,3112
Polymers78,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area6260 Å2
MethodPISA
3
E: A118 serine integrase
F: A118 serine integrase


Theoretical massNumber of molelcules
Total (without water)78,3112
Polymers78,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1060 Å2
ΔGint-6 kcal/mol
Surface area7020 Å2
MethodPISA
4
G: A118 serine integrase
H: A118 serine integrase


Theoretical massNumber of molelcules
Total (without water)78,3112
Polymers78,3112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1230 Å2
ΔGint-9 kcal/mol
Surface area6330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.017, 98.017, 52.587
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

-
Components

#1: Protein
A118 serine integrase


Mass: 39155.633 Da / Num. of mol.: 8 / Fragment: coiled-coil domain (UNP residues 133-452)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria innocua (bacteria) / Gene: int / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q928V6
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 779 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

Crystal growTemperature: 294.16 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.8-1.2 M Na Citrate

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jun 3, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.541→50 Å / Num. obs: 16440 / % possible obs: 98.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 67 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 12.9
Reflection shellResolution: 2.541→2.64 Å / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 1.95 / % possible all: 99.8

-
Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KIS

4kis


Resolution: 2.541→35.853 Å / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.79 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2651 805 4.9 %
Rwork0.2524 --
obs0.2554 16421 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.541→35.853 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3102 0 0 779 3881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023142
X-RAY DIFFRACTIONf_angle_d0.4234203
X-RAY DIFFRACTIONf_dihedral_angle_d11.8141213
X-RAY DIFFRACTIONf_chiral_restr0.017449
X-RAY DIFFRACTIONf_plane_restr0.001540
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.541-2.70010.40981200.40972536X-RAY DIFFRACTION92
2.7001-2.90840.42531360.38852622X-RAY DIFFRACTION95
2.9084-3.20080.35251460.35112614X-RAY DIFFRACTION95
3.2008-3.66330.29741380.30522623X-RAY DIFFRACTION95
3.6633-4.6130.23521360.23642576X-RAY DIFFRACTION92
4.613-30.9980.22951240.2032627X-RAY DIFFRACTION92

+
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