[English] 日本語
Yorodumi
- PDB-5zgn: The crystal structure of KacTA-DNA complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5zgn
TitleThe crystal structure of KacTA-DNA complex
Components
  • (DNA (27-MER)) x 2
  • KacA
  • KacT
KeywordsTOXIN / KacT / KacA / Complex
Function / homology
Function and homology information


acyltransferase activity, transferring groups other than amino-acyl groups / regulation of DNA-templated transcription
Similarity search - Function
Vibrio phage ICP1, Orf50 / Antitoxin TacA 1-like / Acetyltransferase (GNAT) domain / Ribbon-helix-helix / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase
Similarity search - Domain/homology
DNA / DNA (> 10) / DUF1778 domain-containing protein / GCN5-related N-acetyltransferase
Similarity search - Component
Biological speciesKlebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsQian, H.L. / Yao, Q.Q. / Gan, J.H. / Ou, H.Y.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology2015CB554202 China
CitationJournal: To Be Published
Title: The crystal structure of KacTA-DNA complex
Authors: Qian, H.L. / Yao, Q.Q. / Gan, J.H. / Ou, H.Y.
History
DepositionMar 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: KacA
B: KacA
C: KacT
D: KacA
E: KacA
F: KacT
G: DNA (27-MER)
H: DNA (27-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,67211
Polymers97,3848
Non-polymers2883
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area26380 Å2
ΔGint-208 kcal/mol
Surface area35050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.046, 62.044, 61.994
Angle α, β, γ (deg.)93.83, 93.99, 93.93
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 2 types, 6 molecules ABDECF

#1: Protein
KacA


Mass: 10152.146 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: KacA
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_05880
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: A0A0H3GLZ1
#2: Protein KacT


Mass: 20093.129 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Klebsiella pneumoniae subsp. pneumoniae HS11286 (bacteria)
Strain: HS11286 / Gene: KPHS_05890
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: A0A0H3GMP0

-
DNA chain , 2 types, 2 molecules GH

#3: DNA chain DNA (27-MER)


Mass: 8323.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (27-MER)


Mass: 8265.356 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 2 types, 54 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.06 % / Description: rod
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.05M ammonium sulfate, 0.05M BIS-TRIS pH 6.5, 30% pentaerythritol ethoxylate (15/4 EO/OH)

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 20, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.24→30 Å / Num. obs: 38226 / % possible obs: 94.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.4
Reflection shellResolution: 2.24→2.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.311 / % possible all: 92.1

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
AutoSolphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.24→28.44 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 2.05 / Phase error: 28.35
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.255 1862 4.87 %
Rwork0.214 --
obs0.216 38196 93.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.24→28.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4851 1101 15 51 6018
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046183
X-RAY DIFFRACTIONf_angle_d0.8328592
X-RAY DIFFRACTIONf_dihedral_angle_d22.353547
X-RAY DIFFRACTIONf_chiral_restr0.068984
X-RAY DIFFRACTIONf_plane_restr0.004919
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2369-2.29740.34141350.31192641X-RAY DIFFRACTION88
2.2974-2.3650.33481510.29852734X-RAY DIFFRACTION93
2.365-2.44130.30471560.28962706X-RAY DIFFRACTION92
2.4413-2.52850.30961400.27792651X-RAY DIFFRACTION89
2.5285-2.62960.30591740.2652829X-RAY DIFFRACTION95
2.6296-2.74920.2761250.26692842X-RAY DIFFRACTION95
2.7492-2.8940.25391530.25492858X-RAY DIFFRACTION95
2.894-3.07510.30791390.25232821X-RAY DIFFRACTION95
3.0751-3.31220.29041690.25032737X-RAY DIFFRACTION92
3.3122-3.6450.30591620.22012922X-RAY DIFFRACTION98
3.645-4.1710.2461330.19532888X-RAY DIFFRACTION97
4.171-5.24960.18921150.18292833X-RAY DIFFRACTION94
5.2496-28.43770.23331100.18142872X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 56.1852 Å / Origin y: -10.6855 Å / Origin z: 65.3312 Å
111213212223313233
T0.2993 Å2-0.0402 Å2-0.0244 Å2-0.3885 Å2-0.09 Å2--0.3821 Å2
L1.2619 °2-0.3532 °2-0.4128 °2-0.5873 °2-0.0112 °2--0.5007 °2
S0.0559 Å °-0.0005 Å °0.0047 Å °0.0055 Å °-0.0247 Å °-0.0188 Å °-0.0093 Å °-0.033 Å °-0.0409 Å °
Refinement TLS groupSelection details: ALL

+
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